Local government minister Jahangir Kabir Nanak said Mohammed Sohel Rana was arrested at the Indian border.
He has been in hiding since the Rana Plaza collapsed on Wednesday.
Rescuers are in a race against time to reach nine survivors as officials prepare to bring in heavy machinery to move the wreckage.
Mr Nanak said that Mohammed Sohel Rana was arrested near the land-crossing in Benapole along the border with India’s West Bengal state and was being brought back to Dhaka by helicopter.
He made the announcement by loudspeaker at the site of the collapsed eight-storey building in the Dhaka suburb of Savar.
He said the arrest had been made by soldiers from the Rapid Action Battalion.
The BBC’s Anbarasan Ethirajan in Dhaka said rescue workers cheered and clapped at the news.
There has been widespread anger at the disaster and six people, including three factory owners, have now been arrested. The building housed several garment factories.
More than 360 people are now known to have died in the disaster and hundreds more are missing.
On Sunday, two more people were pulled alive from the rubble and a group of about nine survivors was also located.