Warriors chief executive Leighton Samuel says he withdrew his offer to sell his 50% share to the Welsh Rugby Union before the deal was done.
"Just after 1400 BST (on Wednesday) we advised the Union that the agreement was not going to go ahead," he said.
The WRU still maintains it owns the whole of the region, but Samuel says the deadline to pay up was missed.
"We never received the funds until 1455 BST, which we consider to be too late. The deal is null and void," he said.
WRU group chief executive David Moffett says there was never a deadline to transfer the funds to Samuel, and having paid Samuel in full on Wednesday, the Union now legally owns the Warriors.
"The money was in his (Samuel's) account by 1445 BST today (Wednesday)," Moffett told BBC Wales.
"It's all there, it's all in his account. As far as we're concerned that deal is done.
"We are now 100% shareholders of the Warriors and we're going to start behaving that way and we will be seeking all the information from them as a mater of urgency."
The WRU, who already owns 50% of the Warriors' shares, is expected to disband the region because it has repeatedly stated its belief that Wales only has the playing and financial resources to sustain four regional sides.
The first steps to do so seemed to have been taken on Tuesday when the Union met the current Warriors squad to discuss their futures.
That move angered Samuel, who accused the WRU of breaking a promise to keep the team alive. He then promised to do "everything in his power" to save the region from a WRU cull.
"We were annoyed yesterday because we had a Union that had gone literally into a company, stripped the company of its assets and had no right to do so," Samuel said in a press conference on Wednesday.
He added: "On Monday, they (the WRU) told the players they didn't know whether they would be paid, whether the contracts were going to be honoured, which I think is disgusting.
"Yesterday (Tuesday) was even worse. It was like a meat market when the players were lined up and being fought over by four coaches. That was unacceptable."