Carlos Agostinho do Rosário ended up using a military plane for his official holiday through the capital, Maputo, to the Niassa province.
The state-owned airline features been experiencing a cash crunch.
Local media report the “chaos” has recently been going on for three days.
Reports say that fuel suppliers had inquired for payment to be made in advance of delivery.
The airline called the unpleasant incident “embarrassing” but said, it had been working in order to ensure flights resumed on Friday immediately after the government’s intervention, the BBC’s Jose Tembe in Maputo reports.
It apologized to its customers and urged travelers to telephone to get information in relation to their flights.
A six-year ban upon the airline operating in the European Union was lifted last year. It had been imposed because of precisely what the EU said was an absence of oversight by aviation authorities.
Mozambique has been facing a financial turmoil since 2015 and has been mainly cut off from multilateral and overseas donors after the government admitted in order to $1. 4bn (£1bn) of undisclosed credit in 2016.
