The money, handed over just over a week ago, was an initial installment of hundreds of millions of PNG kina that Bougainville says the national government is constitutionally obliged to pay it.
President John Momis said it was another sign that the Peter O'Neill administration did not care about the autonomous region's upcoming independence referendum.
Both Bougainville and PNG were required to fully implement the Bougainville Peace Agreement of which the referendum is a key part, Mr Momis said.
But Port Moresby wasn't prepared to pick up its "end of the stick.
"They keep on procrastinating and who is going to force us to implement it? The United Nations or Australia and New Zealand, the friendly countries?" Mr Momis said.
"We have done everything possible on our side and the national government just keeps on procrastinating, using all sorts of excuses," he said.
The president said he hoped some key issues could be remedied at another meeting with the national government next week.
In the meantime, the Bougainville government was holding onto the cheque in the hope the funds would eventually be made available, Mr Momis said.
However, PNG media is reporting that a cheque the national government gave Bougainville has now cleared.
On Wednesday the President of Bougainville John Momis said the $US1.49 million dollar cheque, given by Prime Minister Peter O'Neill at the end of the Joint Supervisory Board meeting at the end of last month, had bounced.
The money was intended as an initial payment towards preparations for the referendum on independence planned for next year, and Mr Momis said the cheque failing to clear was an indication of the national government's apparent lack of commitment to the vote process.
But Loop PNG reported Mr O'Neill saying to avoid fraud the cheque required a covering letter from the secretary of finance before it could be cleared, and that Bougainville would have known this was the case.
Mr O'Neill is reported to have called an earlier RNZ Pacific story "fake news" but it was from information directly from the Bougainville president.
Source: Radio New Zealand Pacific