Karthikeyan will replace Bruno Senna for Hispania in 2011
Hispania Racing are no longer in the Formula 1 teams' umbrella group.
The back-of-the-grid outfit said they left Fota last month because its agenda was focused more on the leading teams.
"We left Fota around December 15," a spokeswoman said. "For our interests it's better not to be there. It's more for the big teams than the small ones."
But Fota secretary general Simone Perillo told Reuters news agency that Hispania "did not fulfil their 2010 Fota membership fee obligations".
The other 11 teams remain members of the organisation which allows them to speak as a united group in talks with governing body the FIA.
Fota, chaired by McLaren principal Martin Whitmarsh with Ferrari's Stefano Domenicali as his deputy, has in place a 'resource restriction agreement' between teams designed to limit their spending and cut the costs of competing.
The teams are seeking a new agreement to run from 2011 to 2017 but a consensus has been hard to reach on budget limits and what falls within the spending restrictions.
Newcomers Hispania, who struggled to make the starting grid for the first race of the 2010 season, are considered to have the smallest budget of any team and their future has been under considerable scrutiny.
However, team principal Colin Kolles said they would be present at pre-season testing and there were no doubts about their participation.
The team last week announced that Indian Narain Karthikeyan would be one of their two drivers.