On Wednesday last week, Air Partner appointed PwC to do an independent review of the firm after discovering the issue relating to its accounting for receivables and deferred incomes.
On Friday Morris handed in his resignation, which the company accepted with immediate effect.
Morris had been at the company since 2013, initially joining as interim financial controller before becoming acting CFO and eventually CFO.
The firm said in a statement that Morris would remain available for the ongoing independent accounting review.
The company is reviewing candidates to replace him with immediate effect and has engaged a consultancy to assist in this.
In its statement last Wednesday, Air Partner stated that it had found an accounting blackhole relating to the collection of receivables from customers, which dated as far back as 2011.