However, asked about the possibility of a coastguard or other non-nuclear ship visiting New Zealand, Mr Panetta - the first US Defence Secretary to visit since 1982 - said progress was a matter of "one step at a time".
"We've taken some important first steps, and let's see where that takes us in the future."
He said both countries acknowledged differences of opinion in "limited areas".
"Today we have affirmed that we are embarking on a new course in our relationship that will not let these differences stand in the way of greater engagement on security issues."
Yesterday's change in policy should prevent a repeat of the situation in Pearl Harbour earlier this year when New Zealand's naval vessels in the biennial Rimpac exercise had to berth at a civilian dock at Honolulu while other nations were at Pearl Harbour.
New Zealand's Chief of Defence Force, Rhys Jones, welcomed the change, saying it allowed New Zealand to work more closely with others.
He also joked about the Pearl Harbour incident, which had meant New Zealand's navy were closer to Honolulu's restaurants and bars than their counterparts.
"My biggest concern is breaking the news to the sailors that they won't be berthing in Honolulu any more - they'll be out in military bases further away."
Defence Minister Jonathan Coleman said New Zealand had been clear it would not shift its anti-nuclear stance but that did not prevent cooperation, as shown by the increasing number of joint exercises.
The willingness to look past the issue on the part of the United States could be partly because of sensitivity to China's increased presence in the South Pacific.
Mr Panetta visited China last week and invited China's military to take part in the Rimpac exercise in 2014 - previously it has only attended as an observer.
The Defence Secretary said he believed the key to providing for security and prosperity in the Pacific region was going to be the bilateral relationship between the US and China - and military to military relationships were important to that.
Mr Panetta will meet Prime Minister John Key today before leaving the country.
Mr Key said he did not believe New Zealand was in a turf war between the US and China, saying its relationships with the two countries were very different partly because of the historic links with the United States.
"We don't see it as an either/or - we've got a very good relationship with China and we've got an outstanding relationship with the US."
Mr Panetta said there were more opportunities to work together, especially as the United States refocused its attention on the Asia Pacific region. Areas included greater co-operation in the South Pacific, especially in maritime security and surveillance, and working with other countries in peacekeeping and humanitarian and disaster relief.
US will hunt Kiwis' killers
United States forces will go after the insurgents responsible for attacks that killed New Zealand soldiers in Afghanistan if credible intelligence is found, US Defence Secretary Leon Panetta says.
This week, Prime Minister John Key revealed that four SAS soldiers had been sent to Afghanistan to gather intelligence on the insurgents behind two attacks in the northern part of Bamiyan province in which five New Zealand soldiers were killed.
He said it was likely that the US would carry out any counterattack once the insurgents were tracked.
Mr Panetta said the US always committed itself to "going after" those who attacked coalition forces if there was an opportunity.
"We will do whatever we have to do in co-operation with the forces of New Zealand to make sure that they understand nobody attacks our forces and gets away with it."
Mr Panetta said the United States was "profoundly grateful" to New Zealand, which had enabled an easier handover in Bamiyan, where NZ soldiers have been based.
He laid a wreath at the Auckland War Memorial Museum and presented medals to five Defence Force personnel who served in Afghanistan.
