Senior party officials called in the police after the money, thought to have come mainly from subscriptions, disappeared from their Edinburgh offices over the last year.
The missing funds were discovered after a routine financial check, and officers are understood to be investigating a string of accounts to try to trace the money.
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Hide AdThe missing funds have sparked a financial crisis, and forced the party to ask donors including Rangers owner Sir David Murray for help covering the shortfall.
A source within the Conservatives was reported to have said: "The whole thing has been a major embarrassment. It has shown the accounting system was not too robust – which is why no-one noticed until it was too late."