Squirrel P2P Trustee and Squirrel Money are a part of Squirrel Group, which also provides mortgage broker services.
The authority said custodians were required to obtain an assurance engagement with a qualified auditor within four months after the end of a financial year or other relevant date.
Its director of supervision, James Greig, said assurance engagements were a "critical backstop" to make sure a custodian fulfilled its role and investor money was being held appropriately.
"Failure to obtain an assurance engagement can result in significant client harm because the custodian may not identify and address any deficiencies in its processes, procedures, and controls," Greig said.
"Squirrel P2P Trustee Limited should have been aware of these custodian regulations."
Squirrel Money had just over 1400 peer-to-peer clients and $35.5 million of investor funds at the end of March, the authority said.
It said Squirrel complied with the regulations in 2021.
Squirrel chief executive John Bolton said when the company started peer-to-peer lending, it was not picked up as a requirement as part of its compliance programme.
"We were alerted to this in May this year by the FMA and filed one with them. We acknowledged the oversight and got the assurance review completed for our most recent financial year, so we are currently in a compliant state. The report found no issues.
"We take our compliance obligations very seriously and are disappointed to have missed the requirement."
- RNZ
