Guinea-Bissau's attorney general ordered the arrest of the recently-resigned interior minister on Saturday for suspected involvement in the boarding of a group of Syrians with allegedly false passports on a flight to Portugal.
Portuguese flag-carrier TAP suspended flights between the two nations when one of its aircraft from Bissau arrived in Lisbon on December 10 with the group of 74 refugees.
Antonio Suka Tchama, who is believed to have facilitated the Syrians' embarkation, announced his resignation over the affair on December 18 but has not admitted any wrongdoing.
"We have evidence that it is the minister who demanded, directly threatening the station manager, the forced embarkment of 74 Syrian refugees on board a TAP flight," said a statement from Attorney General Abdu Mane, ordering Tchama's arrest.
Armando Namontche, the head of Guinea-Bissau's federal police, refused to detain Tchama on Saturday, however, pointing to a security issue without elaborating.
A source close to the interior ministry said Tchama continues to perform his functions despite resigning.
He was the second senior government official to lose his job over the affair, after then-foreign minister Fernando Delfim da Silva announced 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.
Government spokesman Fernando Vaz told a news conference on December 12 that TAP had "confused commercial issues and politics" and risked being banned from Guinea-Bissau air space.
A police source in Bissau told AFP 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.