Services of the Indian Visa Application Centre (IVAC) in Dhaka and Satkhira were suspended on security grounds on Tuesday, after visa-seekers staged demonstrations on Monday.
The services will also remain suspended today (Wednesday).
The IVAC authorities informed the development to the applicants via mobile phone SMS and its website on Monday.
However, many applicants came to collect their passports on Tuesday without knowing the announcement ahead of their arrival.
During a visit to the IVAC at Jamuna Future Park on Progoti Sharani of the capital, this correspondent found that the entrance to the visa centre was under lock and key while applicants were trying to realise situation there.
Some of them said the IVAC, Dhaka resumed operations on Tuesday to return the applicants' passports.
However, a section of visa seekers staged a demonstration inside the visa centre on Monday noon.
Meanwhile, the Indian High Commission has requested the Bangladesh government to take additional security measures.
The IVAC sent SMS to the visa applicants' mobile phones on Monday night as well as it notified the update on its website and Facebook page.
However, many visa applicants came to the IVAC all throughout the office hour on Tuesday.
Security personnel of the Jamuna Future Park said several IVAC officials came in the morning, but left soon keeping the visa centre under lock and key.
"Passports have been returned as the Indian High Commission in Dhaka remained closed. Your visa application will be re-processed and notified via SMS when the office opens later," an IVAC notification reads.
"Due to limited operations, the visa process may take a longer time. Hence, we are returning passports now and it will be re-processed once operations resume. The applicant will be notified via SMS for resubmit his/her passport," another notification said.
No officials were available at the IVAC to deal with the influx of applicants who were looking for someone to know when the IVAC will reopen.
A medical visa applicant, Sheikh Ilias, came to the IVAC from Gopalganj.
"I've travelled a long distance as I got a SMS on Sunday to collect my travel document, however now found it closed," he said, adding that he intended to go to India for treating his knee pain.
The Jamuna Future Park authorities were seen beefing up security measures in and around the IVAC around 12:30pm on Tuesday.
"We're not part of the IVAC, but we are tired of dealing the visa aspirants," one official told the FE.
There was no IVAC official to confirm whether it will resume operations tomorrow (Wednesday), he said.
According to sources, nearly 2.5 million Bangladeshis travel to India every year in various categories, including tourists, medical, education and business visa.
However, after the start of the quota reform movement in mid-July, the visa process was restricted.
The IVACs remained closed since August 4 due to an unstable situation in Bangladesh. Now visa centres are open on a limited basis, but no new applications are being accepted.
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