Preo Bala Biswas, the Executive Director of the Self-Help Association for Rural People through Education and Entrepreneurship (SHAREE), met Trump at the White House on July 17 as part of a global forum.
In a statement on Saturday, Bangladesh's Foreign Ministry said her allegations were "blatant lies", Efe news reported.
"It appears that there was an ulterior motive behind Saha's (Biswas) absolutely false and concocted stories that were targeted to malign Bangladesh," the statement said.
During the brief meeting between Biswas and Trump, she called on the US President for help prevent the disappearance of members of religious minorities in the predominantly Muslim country.
A video of the exchange, which went viral, shows Biswas telling Trump: "I am from Bangladesh. Here 37 million Hindus, Buddhists and Christ disappeared. Please help us... We want to stay in our country. Still there is 18 million minority people."
She continued: "Please help us. We do not want to leave our country. Just help up to stay. I have lost my home. They burnt my home and they have taken my land but there is no justice in sight."
Bangladeshi Minister of Home Affairs Asaduzzaman Khan told reporters the activist would be questioned over her claims upon her return to the country.
"Once she is back of course we will ask. I think there is a motive behind disseminating this untrue news, we have to see what her motive was," Khan said.
The General Secretary of the Bangladesh Hindu Buddhist Christian Unity Council Rana Dasgupta said that it was unclear what Biswas had "meant with the word disappear", but pointed out many Hindus had migrated to India over the years.
"In 1947, the minority population was 29.7 per cent, which came down to 19-20 per cent in 1970, and according to Bangladesh census in 2011 it was 9.7 per cent," he said.
More than 90 per cent of the population of Bangladesh is Muslim.
( With inputs from IANS )