There were questions about it from journalists.
Clinton's excuse was that it had been a recommended to him under United States law by their International Trade Commission, that it was within the rules of the World Trade Organisation and that New Zealand was free to appeal the decision (which it did - and won).
There was a jolly good joke between him and then-Prime Minister Jenny Shipley about how he had eaten up all his lamb at lunch.
There was also a question asking what he thought about the "P5."
It was a new concept, a free trade agreement (FTA) proposed by New Zealand between five Pacific countries - New Zealand, Singapore, Australia, Chile and the United States.
Clinton told the press conference it was "a very interesting idea" and he would get back to Shipley on it in a couple of weeks.
A bit like the cheque in the mail, the "good news" never arrived.
The US did not accept the 1999 invitation to join a P5 because the Clinton Administration's top priority was to convince Congress to approve China's accession to the WTO.
The P5 proposal was the baby of Lockwood Smith, the devoted and passionate trade minister, and now Parliament's Speaker.
Smith concluded that Apec, though promoting the goals of free trade, was not a suitable forum in which to negotiate free trade deals, so he invited his Singapore counterpart, George Yeo, to embark on an FTA with New Zealand.
That's where it began. Lead negotiator was one Tim Groser, now the Trade Minister. A high-quality bilateral deal between New Zealand and Singapore was signed in 2001.
Chile and Brunei joined a couple of years later but the deal, officially called the Trans Pacific Strategic Economic Partnership - P4 for short - was closed off without concluding an investment and financial services chapter.
There are 11 countries now negotiating in San Diego: New Zealand, Singapore, Chile, Brunei, the United States, Australia, Peru, Vietnam, Malaysia - and newcomers Mexico and Canada, who will have to sign up to the parts that have already been agreed.
Groser says the negotiation has developed a genuine momentum.
It was like deciding which restaurant to go to - "the one where people are queued up outside or one where you can have a table because there's a whole lot of empty tables", he says.
"All the people are queuing up outside the TPP restaurant right now and that's the one everyone wants to go."
The world's third-largest economy, Japan, is still considering whether to join.
If that happens, says Groser "this then becomes bigger than King Kong".
By 2008, things had changed for the United States. Distracted by the wars in Iraq and Afghanistan it had taken its eye off Asia and was looking to reassert its strength in the region, not least economically, with China's might rising.
When it heard the P4 group was about to re-embark on negotiations to conclude the investment and financial services chapter, it asked if it could join in too.
Phil Goff was Trade Minister and his response was that it was all or nothing. So all it was. The US was bolstered with three additional applicants, Australia, Peru and Vietnam.
The TPP is now the only trade deal Barack Obama's Government is pursuing and the US is now the power behind the deal, with New Zealand working closely in support as the official adminstrator.
It is certain to be part of Obama's "growth story" in the campaign for the presidential election in November, with ongoing concerns about sluggish recovery from the global financial crisis.
Each round is a huge exercise. More than 500 officials, divided into groups, negotiate the highly legalistic text of 28 chapters.
New Zealand's delegation of about 30 to San Diego is led by David Walker. He has at least one person in each negotiating group but for more important groups, such as the chapter on intellectual property, there could be five or six.
The way it works is that anything that's not in brackets has been agreed to. Anything in brackets requires more negotiation.
New Zealand has had plenty of experience in the World Trade Organisation, as well as in free trade deals with Thailand, China, Malaysia, Hong Kong and Asean, and others under way with Russia, Korea and India.
Groser calls the New Zealand negotiators "the All Blacks" of international trade policy.
"For 40 years we've had a whole cadre of New Zealanders who are as good as anybody in the world at this
game. They have produced astonishing results out of almost nothing, actually." In Geneva, he says, they call it the "New Zealandisation" of international trade law.
George W. Bush's former trade envoy, Susan Schwab, backed that up in an interview with the Herald last year, saying the value New Zealand brought to trade negotiations was not what it could offer but its advocacy for "a very high quality, high bar outcome. That is the fundamental importance of the role that New Zealand can play."
It can also lay claim to having a fair degree of strategic nous.
The transition of the New Zealand-Singapore deal into the TPP was not an accident of fate. There is clear evidence it was a plan manufactured in New Zealand 13 years ago.
While the US was considering the P5 invitation, Lockwood Smith made a speech at the Northern Club in Auckland, which set out the long-term strategy.
The deal wasn't about New Zealand and Singapore, two small countries already committed to free trade and "right at the top of the league tables when it comes to economic freedom and openness".
He said it was to be a model for the rest of the world and the benefits would increase as others joined.
Smith also set out the end goal for what he described as a very simple FTA: it would cover goods, services and investment; there would be no tariffs or export subsidies; and no non-tariff barriers. Government procurement would be fair, Customs would be simplified, standards made to conform, intellectual property protected and competition principles developed. Exceptions to the agreement would be limited.
"The idea is that it should be the ultimate free trade agreement - even more comprehensive and simple than our CER [Closer Economic Relations] with Australia."
Groser says the officials are making good progress and should have what he calls the "undergrowth" cleared away this year, ready for the much tougher stuff next year around issues such as intellectual property, agriculture and investor-state disputes procedures.
But this time next year, he says it should be clear whether it will be a success or a failure. He doesn't rule out failure because he says New Zealand wants a "gold standard" agreement - "and this time we mean it".
New Zealand had a wonderful FTA with China and Asean and others. We don't need a second-rate agreement with anyone any longer. We've got options, for the first time in 35 years."
Getting rid of tariffs was essential. New Zealand would agree to "massive flexibility" about the phasing-in but, he says "the bottom line is tariff elimination".
That will clearly have to include the remaining tariffs on New Zealand lamb, Mr Clinton.
