Police said they are "working with all faith groups" after complaints that worshippers were being "intimidated" by young people in Prestwich.
A video which has been circulated widely shows a woman driving up to the Masjid-e-Bilal on Bury New Road.
She is greeted by very loud music and a van with flashing lights. A teenager carrying a fake gun and wearing a boiler suit gestures towards the woman as she slowly passes.
The youths are from a Jewish background and worshippers say the actions have been "provocative".
The video is accompanied by a message saying: “A number of young people have been dressed in red and blue boiler suits. We have reported and logged with police.”
Another message says people will be "standing outside the masjid, in solidarity and keeping the masjid and the congregation safe".
Greater Manchester Police Assistant Chief Constable Wasim Chaudhry said: “We’re aware of a video circulating online that’s believed to have been filmed close to Prestwich Mosque earlier this week, which has caused concerns.
“We’re investigating the circumstances behind it, and we are patrolling local areas to help people feel safe in their communities.
“Our local neighbourhood teams continue to work closely with all communities and faith groups to address concerns together. Information from the public is also crucial and any concerns should be reported directly to us via 101 or by visiting the ‘Your Area’ pages of our website – gmp.police.uk.”
In a statement the Greater Manchester Council of Mosques (GMCoM) said the "isolated incidents do not reflect the positive relationship that exists between the Muslim and Jewish communities in Greater Manchester".
They said "such actions not only undermine the sanctity of places of worship but also threaten the fabric of our diverse community".
Co-chair of GMCoM, Asif Patel said: ‘’We are deeply troubled by the recent targeting of Bilal Mosque in Prestwich. Such actions not only undermine the sanctity of places of worship but also threaten the fabric of our diverse community.
"GMCoM stands in solidarity with Bilal Mosque and its congregation, and we are committed to working closely with them and the authorities to ensure the safety and well-being of all.
"Let us remember the values of unity and respect that bind us together as a community and let us strive to overcome these challenges with resilience and compassion.
"Together, we must continue to foster understanding, dialogue, and cooperation for the greater good of our shared community. We urge anyone with information regarding these incidents to come forward and assist the authorities in their investigation."
Masjid-e-Bilal have been approached for comment.
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