The Ministry of Natural Resources and Environment and the Ministry of Works, Transport and Infrastructure were being investigated, according to a report in the Samoa Observer.
The environment ministry's CEO, Ulu Bismarck Crawley, confirmed the investigation but would not disclose the amount of money missing.
Ulu said three employees implicated had been reassigned to other divisions of the ministry while they awaited the outcome of the investigation.
The investigation into the Ministry of Works, Transport and Infrastructure comes as around $US5000 has gone missing.
CEO Afamasaga Su'a Pou Onesemo said cheques amounting to over $US35,000 had already been recovered.