Guinea-Bissau's interior minister announced his resignation on Wednesday after the west African nation allowed a group of Syrians to board a flight to Portugal with allegedly false passports.
Portuguese flag-carrier TAP suspended flights between the two nations last week when one of its aircraft from Bissau arrived in Lisbon with the group of 74 refugees.
"I took the decision to discharge my duties as interior minister so as not to hinder ongoing investigations," Suca Ntchama told a news conference.
Ntchama, a colonel in the air force, is believed to have facilitated the boarding of the Syrians to Lisbon, according to a source familiar with the case.
He is the second senior government official to lose his job over the affair, after Foreign Minister Fernando Delfim da Silva announced last week he was quitting in protest against the implication of government officials and police in wrongdoing.
Seven police officers have since been suspended and a judge-led inquiry has been set up.
The incident sparked a diplomatic row between Bissau and its former colonial power, from which it gained independence in 1974 after a war lasting more than 10 years.
"I'm not surprised by TAP's reaction. It is to be expected from the Portuguese government," government spokesman Fernando Vaz told a news conference last week.
Vaz said TAP had "confused commercial issues and politics" and risked being banned from Guinea-Bissau air space.
Portuguese media have reported that the TAP crew were forced to allow the Syrians to board after being threatened by the Guinea-Bissau authorities.
But an immigration official at Bissau airport told AFP the group, which included 30 children and a pregnant woman, "all had Turkish passports. This is why we let them board."
A police source in Bissau told AFP last week that the Syrians had entered the city via Turkey and Morocco.
Portuguese police said the refugees had been provided housing pending the outcome of asylum applications.
Portugal has never recognised the transitional authorities established in Guinea-Bissau after a military coup that overthrew the government in April last year.