"Huge investments were made for the green factories. But the buyers are not raising prices. They are cutting prices instead," Tofail Ahmed said during a meeting with a delegation of a German trade union on Thursday.
The green factories were developed in an effort to improve workplace environment and safety after the death of over 1,130 people in the Rana Plaza collapse in 2013.
Tofail said seven of 10 factories that received Leadership in Energy and Environmental Design certificates from the Green Building Council of the US were in Bangladesh.
He said all sorts of steps were taken to ensure safety in workplace in the garment factories after the Rana Plaza collapse.
According to him, 39 factories have been shut down and 47 renovated following the buyers' request after inspections into 3,780 factories by Accord, Alliance and National Initiative.
"The number of non-complaint factories is below 2 percent, which is an internationally recognised standard," Tofail said.
He also said the government amended the labour law to ensure workers' rights while steps were taken to stop accidents like Rana Plaza collapse.
He said the government allowed formation of Workers' Welfare Association for about 400,000 workers in export processing zones to let them bargain with the owners.
The commerce minister told the delegation of Germany's Friedrich-Ebert-Stiftung, led by its Vice-Chairman Michael Sommer, that Germany is Bangladesh's second largest market as a country.
German Ambassador Thomas Prinz, Head of FES Department Asia and the Pacific Jürgen Stetten and its Resident Representative in Bangladesh Franziska Korn were also present.