Biman sent the passport of the pilot, Captain Fazal Mahmud, in another flight to Qatar later, Civil Aviation Secretary Mohibul Haque told bdnews24.com on Thursday.
"It will be investigated with due importance how the pilot got on the plane at Hazrat Shahjalal International Airport without a passport," he said.
Biman, the national carrier, will on Friday send another pilot to fly Hasina back, he added.
The Prime Minister is in Finland as part of her official trips to three countries. She had earlier visited Japan and Saudi Arabia.
She is scheduled to return to Bangladesh on Saturday.
A special flight of the flag carrier will ferry Hasina to Dhaka after she will have reached Qatar from Finland by another flight, according to Biman officials.
Fazal flew a Boeing 787 Dreamliner from Dhaka to Qatar on Wednesday night for the prime minister, the officials said.
The issue of him carrying no passport was discovered when the flight reached Qatar.
bdnews24.com contacted the secretary after social media users claimed in posts that the pilot was detained at immigration of Doha International Airport for having no passport on him.
"He was not detained in the incident on Wednesday. He was provided a hotel room to stay," Mohibul said.
( With inputs from IANS )