Maulana Abdus Shakoor, head of the Rauzatun Saliheen Alim Madrassa, said he had received a letter from the authorities asking him to keep the madrassa closed during the one-off test match from June 10-14.
"This is the first time we have received a request from the government administration to keep the complex closed," Maulana Shakoor told AFP.
Test cricket will return to Fatullah stadium after nine years, having hosted its only five-day match against Australia in 2006. The ground has so far hosted 10 one-day internationals, including five matches of the Asia Cup in 2014.
Maulana Shakoor said he was surprised by the diktat as classes in the seminary were held during the Asia Cup last year.
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"But this time we have been asked to declare a vacation for five days. I have got verbal permission only to keep 25 orphans in our dormitory on humanitarian grounds," he said.
Bangladeshi madrassas have been under the spotlight in recent months after two of their students were arrested over the slaughter of an atheist blogger in the heart of the country's capital.
Bangladesh fans were left infuriated when several umpiring decisions went against the cricket minnows, dashing their hope to reach the semifinals for the first time.
The then Bangladeshi president of the International Cricket Council Mustafa Kamal added fuel to the controversy by suggesting the umpires were biased in favour of heavyweights India.
Imam said the authorities have also banned any anti-Indian banners and festoons in the stands during the matches.