The board of the People's Vote campaign has written to the Electoral Commission asking it to investigate donations made to the group under previous management.
The organisation - which wants a second referendum on Brexit - said it believed some payments may not have been declared properly.
People's Vote said it was "extremely concerned" over this suggestion.
Its request for an inquiry follows a dispute over management, which resulted in some senior figures being sacked.
At the end of October, People's Vote's then director, James McGrory, and its head of communications, Tom Baldwin, were dismissed.
Many staff subsequently staged a walkout in protest and refused to return to work.
Two of the youth organisations that made up the People's Vote campaign broke off, while a new group campaigning for another referendum, Final Say, was established with Mr McGrory and Mr Baldwin as advisers.
A People's Vote spokesperson said: "The People's Vote is asking the Electoral Commission to look into possible non-disclosure of donations under the organisation's previous executive management.
"The new interim management team, in place since beginning of November, has been conducting a fundamental review of the organisation's systems, policies and processes.
"In the course of this review we became extremely concerned donations may not have been declared to the Electoral Commission. We immediately made the Commission aware of this."
A spokesperson for the former staff of the People's Vote campaign said: "We are entirely confident that we have always complied with the Electoral Commission's reporting requirements in regulated periods."
They added that it was "deeply disappointing" the current management was "smearing the team who built" People's Leave "in a desperate attempt to avoid taking responsibility for the shambles he has turned this once great campaign into".
An Electoral Commission spokesman said: "The People's Vote has made us aware of potentially unreported donations.
"We have not at present opened an investigation, but we are considering the information they have provided to us."