A Parliamentary Standing Committee has recommended identification of those NGOs after hearing the complaint in a meeting on Thursday, bdnews24 reported.
As the MPs met in Dhaka, a second attempt to send the refugees back to their homeland from camps in Cox's Bazar stalled.
"The Foreign Ministry has informed us that some NGOs are making the Rohingya understand that they should not return to their country," the Committee's Chairman Muhammad Faruk Khan said.
"These NGOs are telling the Rohingya that they should not return unless some conditions, including citizenship, are met.
"The Committee has recommended identification of these NGOs through monitoring," he said.
The Rohingya living in Bangladesh are unwilling to return over fear of more violence that forced them into the country two years ago.
The first attempt to start the repatriation failed around a year after the exodus, bdnews24 reported.
Foreign Minister A.K. Abdul Momen said on Thursday that they would not force anyone to go, but added the Rohingyas' refusal to go back to their homeland was "disappointing" and "unexpected".
The Rohingya, depending on relief materials to fulfil their basic needs in Bangladesh, have set at least four conditions for the repatriation to start - citizenship, security, compensation, and land right.
Besides the UN agencies and the government, local and foreign NGOs are working in the Cox's Bazar refugee camps that have sheltered over 1.1 million Rohingya.
( With inputs from IANS )