Force India and Sauber say the way revenues are divided and rules decided is "unfair" and have asked the EU's Competition Commission to investigate.
Formula 1 generates £1.1bn of income, of which 63% goes to the teams.
The Competition Commission told BBC Sport it would now decide whether the complaint merited a full investigation.
In a statement, Force India said: "Sahara Force India is one of two teams to have registered a complaint with the European Union questioning the governance of Formula 1 and showing that the system of dividing revenues and determining how Formula 1's rules are set is both unfair and unlawful.
"Due to the ongoing legal discussions, it would be inappropriate to comment further at this time."
F1 chief executive Bernie Ecclestone had previously said he would welcome such an investigation because he feels the sport has nothing to hide.
Ecclestone also asked why teams had signed contracts with F1 if they had cause for complaint.
Earlier this year, Labour MEP Anneliese Dodds said she had "real concerns" about the plight of smaller teams in the sport, but added that the Competition Commission would only investigate after the teams themselves had submitted a formal complaint.
"At Force India I saw just what a great role F1 can play in creating the kind of high-quality jobs in science and engineering that we want to see much more of as a country," she said. "We simply cannot afford to lose those kinds of jobs."
Last season saw hundreds of jobs go with the collapse of the Caterham F1 team, while Marussia also went into administration before new investors intervened to create the Manor Marussia outfit.
Renault this week announced that it was taking the first steps towards a buy-out of cash-strapped F1 team Lotus.
However, Ferrari president Sergio Marchionne, a trained lawyer, said he believed there was "limited scope" for the commission to intervene.
The Italian team receive special payments to reflect their status as the oldest and most successful outfit in F1.
"These things are incredibly clear deals, they are evident and they have been publicised," he said. "If it happens, we'll deal with it but I doubt very much that it will go very far."
Two of Formula 1's smallest teams have accused the sport of being run "unlawfully" in a complaint to the European Union.