Stefano Domenicali said FOTA was pushed beyond the point where it could consider compromising its stance and entering next year's world championship under the FIA's terms.
The eight teams still active in the teams' alliance declared last Thursday night that they would establish their own breakaway series next season.
Although FIA president Max Mosley said yesterday that there was much common ground and a deal could easily be reached, Ross Brawn responded that FOTA would prefer to press ahead with its rival championship rather than return to the table with the FIA.
Domenicali agreed with Brawn's position and said the time for talking was over.
"Ross spoke not only for Ross, but for the FOTA teams – that's the line of all the teams," he said.
"We want to go ahead with the [breakaway] project and we want to show it as soon as we are ready.
"Our position is pretty clear. We've put some conditions on it, and that's it.
"All the FOTA teams have shown a great respect for the FIA and a lot of will to find solutions and compromise.
"But there is a limit and you have to act accordingly.
"I think we have shown a very rational and professional approach."
While Mosley suggested that there were 'elements' in FOTA that were more committed to the breakaway cause and others willing to compromise, Domenicali said he was fairly sure that the teams were in total agreement.
"I don't exclude anything because in life and politics we know how things work – in front of the sheen and behind the sheen," he said.
"But the position of FOTA is pretty clear and I was very happy to see we were very united on this position."
Domenicali added that while Ferrari in particular had been very critical of the new teams lining up to either replace the FOTA squads in the F1 entry or take some of the vacant spaces, FOTA would be happy to work with newcomers in its breakaway championship – provided they were of suitable calibre.
"We'll be able to make sure that the big constuctors, the independent teams and the new teams that want to come in are very, very welcome," he said.
"This is something that has to be very clear: no one is putting any kind of barrier to new teams.
"We are very happy to have new teams, but the value of Formula 1 must not be devalued by the level of new teams that want to come in, with all due respect."