An investigation, however, revealed that the marks were painted by the civic body's sanitation staff.
The city police swung into action after residents of one such society in Paldi area here wrote a letter yesterday to the Election Commission and the city's police commissioner, urging them to inquire the matter.
The residents wrote in the letter that they feared it (putting the marks) was done with a "clear purpose to identify Muslims living in that area" ahead of the assembly polls in Gujarat next month.
"The Ahmedabad Municipal Corporation staff visited the area with us yesterday and informed the residents that it is part of their garbage collection project," Paldi's police inspector B S Rabari said.
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"The cross marks would help the sanitation supervisors to identify those societies which would be covered under their GPS-based waste collection system. There is no reason for residents to panic," he said.
After the probe, the police said, it learnt that such cross marks in red colour were painted not only in Muslim societies but also on the gates of Hindu societies in Paldi area for the implementation of the waste collection project by the Ahmedabad Municipal Corporation (AMC) staff.
"Such activities of marking buildings of a particular community and highlighting their religious identity before the election is causing insecurity among the dwellers and increases chances of communal clash which might destroy peace of Paldi...take immediate action and investigate the reasons," reads the letter penned by members of the society.
According to Uvesh Sareshwala, who lives in the building, there was fear and panic among Muslims when they found red marks on the main gates.
"Due to such misunderstandings, miscreants get a chance to disturb the peace. Our only concern was our security, nothing else," Sareshwala added.