Stephen Koukoulas, economic adviser to Illion, said big businesses had always been slower to pay compared to micro businesses - those with fewer than five employees and small to medium sized businesses.
"They have always been a bit tardy."
But he said the increase by large businesses could be seen as a warning that the economy was headed for tougher times.
"It may be just a little bit of an amber light."
Koukoulas said if there were increases in late payments in the next two quarters of data, which were normally seasonally lower, it could be a sign of something more serious and a cause for concern.
"When the country is doing reasonably well - not booming not crashing - it is okay. The problem emerges as the economy slows down.
"One of the things that compounds an economic slow-down is cash-flow and the flow-on effect."
Koukoulas said it last saw an increase in businesses making late payments in Australia during the global financial crisis.
"We saw late payments rise quite sharply."
"When times get tough that compounds the down-turn."
illion chief executive Simon Bligh said small businesses were the engine room of the New Zealand economy but were often at the mercy of the largest companies.
"Compared with Australia, where businesses took more than 10 days to pay overdue invoices, these are much better results, but it's still not right that the majority of Kiwi firms and their cash-flows are dependent on when other businesses get around to paying them."
Big businesses were late in paying their invoices by an average of 9.2 days in the June quarter up 3.4 per cent on last year.
That compared to businesses with between six and 19 employees who had the shortest late payment delay of 5.3 days - down 20.5 per cent on last year.
Forestry businesses were the slowest to pay their invoices, with an average of eight days
while farmers were the fastest and most reliable payers, averaging four days.
The fishing sector showed the biggest improvement, with late payment days decreasing by 38 per cent year-on-year.
Koukoulas said big businesses who were slow to pay smaller businesses created a power imbalance.
"If you have got a relationship with a big business you won't be rocking the boat if they are your main supplier and saying can you pay me."
There have been calls for big business to stop treating small business like banks by paying invoices late - if necessary by regulation.
The Government is also looking into the issue. In December Small Business Minister Stuart Nash and Commerce Minister Kris Faafoi, released a discussion document, which said many small businesses did not have "a fair and healthy" relationship with their suppliers.
They said there was scope for a law change to address some of the issues, which included significant cashflow issues as a result of not being paid by other businesses for several months.
Submissions in response to the discussion paper "Protecting businesses from unfair commercial practices" closed in late February with 44 responses.
Last month Nash said he and Commerce Minister Kris Faafoi would make announcements in the next month or so in response to the discussion document.
Koukoulas said the last five year years more businesses had been paying on time reflecting a structural change made as a result of technology.
In the past businesses would get an invoice, write out a cheque and post it off. Now direct debits and online banking have made payments much faster and he said small businesses had embraced this technology shift, he said.
"The lower level of late payments over the past five years or so reflects a structural change, with businesses increasingly adopting new technologies and systems such as internet banking and direct debits, which have resulted in bills being paid faster.
"The recent stability in payment times reflects conflicting news in the economy – with business cash flows boosted by low interest rates, but hampered by the slowing economy."
