Earlier reports from Greater Manchester Police had suggested the units were responding to calls from a college in Trafford but was later clarified as an incident in Hulme area in the centre of the city.
"Police are responding to a call at a college in Trafford. Officers are in attendance and we are currently assessing the situation.EOD (Explosive Ordnance Disposal) have arrived on site," Greater Manchester Police had said in a statement.
"This has now been deemed safe and the cordon has been removed," police said.
The EOD conducted a search at a block of flats and left the site on Linby Street soon after.
Intense police activity and a major lockdown in the area was later lifted.
The city has been on high alert since Monday's suicide bombing that claimed 22 lives at an Ariana Grande concert in Manchester Arena.
The false alarm came just as the UK held a minute's silence at 11 AM local time in memory of the victims of the attack.
Queen Elizabeth II visited the Royal Manchester Children's Hospital to meet the children injured in the attack and the staff at the hospital.
Her visit is being described as a morale boosting tour for the patients and healthcare professionals caring for them.
Meanwhile, British Prime Minister Theresa May has said the threat level in the UK will remain at "critical".
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