Local government minister Jahangir Kabir Nanak said Mohammed Sohel Rana was arrested at the Indian border.
He had been in hiding since the Rana Plaza collapsed on Wednesday.
Rescuers are in a race against time to reach remaining 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.
Mr Nanak 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.
Bangladeshi TV later showed Mr Rana in handcuffs after being flown back to Dhaka by helicopter.
Group of nine There has been widespread anger at the disaster and six people, including three factory owners and two engineers, have now been arrested. The building housed several garment factories.
By Sunday evening the confirmed death toll had reached 377, but hundreds more are still missing.
Earlier, two more people were pulled alive from the rubble and a group of about nine survivors was also located.
Teams were using light cutting equipment to try to reach them, our correspondent says, and water and food were being dropped to them through gaps in the rubble.
But with hopes fading for those still trapped, officials plan to bring in cranes within the next few hours.
The army officer co-ordinating the rescue, Maj Gen Chowdhury Hasan Suhrawardy, said they would try to save the nine people first by using light equipment.
"But if we fail we will start our next phase within hours," he said.
This would involve using hydraulic cranes and cutters to bore a hole from the top of the collapsed building, he told reporters.
He said they still aimed to recover other survivors as well as bodies.
"We have no other choice but to use some heavy equipment," he said.
"We will start it within a few hours. Manual operation and use of small equipment is not enough."
Police said officials had ordered an evacuation of the building on Tuesday after cracks appeared, but that the factories ignored them and were operating the next day.
Factory bosses Mahbubur Rahman Tapas and Balzul Samad Adnan surrendered to police early on Saturday while Aminul Islam was arrested later the same day.
Thousands of relatives of missing workers are waiting at the site as survivors and the dead are pulled from the rubble.
At least 3,000 are estimated to have been in the building when it collapsed. About 2,430 are now known to have survived.
There is no official figure on the number of people still missing, but Akram Hossain, a deputy director of the fire service, said their chances of survival were "diminishing by the minute".
Anger at the building collapse has triggered days of violent protests in Dhaka.
On Sunday, garment workers blockaded a main road in a nearby industrial zone of Gazipur demanding capital punishment for those responsible.
Bangladesh has one of the largest garment industries in the world, providing cheap clothing for major Western retailers that benefit from its widespread low-cost labour.
But the industry has been widely criticised for its low pay and limited rights given to workers and for the often dangerous working conditions in garment factories.