Goyal founded Jet Airways in 1993 and was its chairman till he was asked to step down by lenders in March.
Jet, which has a debt of over Rs 8,000 crore, shut operations last month, after running short of cash. Banks denied fresh loans as well. Goyal's resignation has come under much criticism and unpaid employees have questioned why banks asked their chairman to step down and not release any funds.
The airline's grounding has left 14,000 employees without pay. The CEO and other senior executives have quit.
A staff union, led by Nationalist Congress Party MLC Kiran Pawaskar, had filed a police complaint seeking restrictions on Goyal and the senior management from leaving India.
Jet is also facing multiple probes by the income-tax department and the corporate affairs ministry for tax evasion and other non-compliance issues. The Enforcement Directorate is also probing the majority sale of its loyalty programme to Etihad Airways.
The development comes as lenders continue to search for an investor. Over half its planes have been repossessed. Lenders and strategic partner Etihad Airways are in discussions with the Hinduja group for a possible revival.