The Scottish Premier League on Monday vowed to hold a vote within 10 days on its plans to merge with the Scottish Football League and instigate play-offs between the top two divisions.
However, it rejected amendments suggested by the 30 SFL clubs involving spreading more money from the second tier to the bottom two divisions.
With the 12 SPL clubs, including relegated Dundee, united, the future of reconstruction plans now appears to lie with the SFL and whether it is prepared to accept changes despite its concerns being dismissed.
The SFA has been involved in the prolonged talks but Regan's offer to mediate was rejected by the SFL last month. And he is keen to see more co-operation as Scottish football looks to overcome the financial strife that has affected Rangers, Dunfermline and is threatening the future of Hearts.
Regan, who this week announced a two-year extension of William Hill's Scottish Cup sponsorship, said: "We have seen financial turmoil at a number of big clubs in Scotland, clubs complaining about the need for finances to survive, First Division clubs writing requesting a desire to go to the SPL largely because of the financial risks they are facing.
"So we are not in a good place. But we are where we are. We have got to look forward and do something about it.
"But it's fair to say we are not in a particularly healthy place and we have to work collaboratively with the leagues, with the clubs, with all of our partners, to try to turn that round."
The SPL's deal with Clydesdale Bank runs out this summer and no replacement has been lined up.
"It's not surprising that with so much uncertainty in the shape of the competition, the number of teams, whether there are play-offs, whether there are one or two leagues, it's not surprising that it's difficult to give certainty to commercial partners," Regan said.