The immigration police said, on November 19, the government gave instruction to passengers returning from abroad to get Covid-19 negative certificates within seven days.
The certificate will be valid for 72 hours, it added.
Benapole check-post was closed to the returnees without Covid-19 certificate on Friday following the direction.
The stranded passengers said they went to India with a Covid-19 negative certificate but they did not know they would have to get the same certificate from India to enter Bangladesh.
Benapole Checkpost Immigration Health Officer Dr Bichitra Mallik said, "We are unable to go against the government direction."
However, a special direction may come regarding those who reached the check-post on Friday, Benapole International Checkpost Immigration Officer-in-Charge Ahsan Habib said.
On November 15, Health Minister Zahid Maleque said passengers returning home from foreign countries must show Covid-19 negative certificates at the immigration.
"They will have to go into quarantine for 14 days upon their return, else."
Also read: Passengers returning from abroad must carry Covid-19 negative certificates: Minister