M Shahidul Haque said they would start the process of taking back 2,415 of its nationals it verified earlier.
The decision was conveyed at the secretary-level talks on Sunday.
Myanmar’s Deputy Foreign Minister U Thant Kyaw led his side to the meeting, known as ‘Foreign Office Consultation’.
Foreign Secretary Haque told journalists after the meeting both sides agreed on a number of measures to take the relations forward.
The meeting was held in “open, frank, and cordial” manner that he said indicated “greater understanding between the two countries”.
Myanmar side was not present at the briefing.
The Rohingya refugee issue has been the main irritant in the relations.
Bangladesh gave shelter to thousands of refugees who fled the Rakhine province after sectarian clashes over the years.
The UN refugee agency, UNHCR, put the number in Bangladesh at over 200,000 with 30,000 documented refugees living in two government-run camps –the Kutupalong and Nayaparha – within two kilometres of the Myanmar border.
Some estimates suggest more than 500,000 are living outside the camps in Bangladesh.
According to the foreign ministry, Myanmar took back more than 200,000 of their nationals between 1991 and 2005.
The process has since stalled and Myanmar even declined to recognise those living inside Bangladesh as its nationals.
The meeting also agreed to release prisoners of both sides.
Official figures show 190 Bangladeshis are languishing in Myanmar jails, while the number is 110 of Myammar nationals in Bangladesh prisons.
The import of gas from the Shwe gas field in the Rakhine state has also been discussed.
A consortium of China, India, Myanmar, and South Korea’s Daewoo has developed the field and about 800 km of pipeline laid to take the gas to Kunming, in China.
Bangladesh has already got a positive response from China for the gas supply while officials said they would try to convince the others.
The foreign secretary said Myanmar also made it clear that they would have no problem in giving gas to Bangladesh provided there was surplus and other partners agreed.
He said the four-hour meeting also felt the home secretaries of the two countries must meet to discuss border issues.
“We all agreed to strengthen the relations,” he said.
Despite decades-old irritants in relations, both Bangladesh and Myanmar work actively at the Bay of Bengal Initiative for Multi-Sectoral Technical and Economic Cooperation (BIMSTEC) grouping.
The talks on the proposed economic corridor under the Bangladesh-China-India-Myanmar (BCIM) formation were underway.
A new idea of forming a Bay community with Bangladesh, India and Myanmar, particularly after the resolution of the maritime boundary dispute, is also gaining ground.
Bangladesh is planning road connectivity between Chittagong and Kunming, capital of China’s Yunnan province, through Myanmar.
The foreign secretary said they had discussed the revival of a committee for this road link.
“We’ll also look into the possibility of one more route (of road connectivity),” he said.
They also decided to ratify the treaty signed in 1999 for border demarcation along the river Naf.
The Secretary said they felt it “extremely important” to have people-to-people contacts.
Myanmar is interested in offering tourism packages with Bangladesh and Kunming.
They renewed the cultural exchange agreement that expired in 2012 for the next five years.
The foreign secretary said Myanmar would send a team shortly to learn from Bangladesh’s agriculture, fishery and livestock sectors.
“Overall, I would say it’s a breakthrough in bilateral relations,” he said.