The Pakistan Sikh Council raised the issue at a news conference at Karachi Press Club. Sardar Ramesh Singh, the Council's head, said five incidents of the holy book being desecrated had been recorded so far.
Most of the incidents occurred inside Hindu temples, where the Guru Granth Sahib is kept as many people from the Hindu community also believe in the teachings of Sikhism, he said.
The first incident occurred at Samadha Ashram in Shikarpur, where a Hindu elder was accused of "drawing pictures" in the Guru Granth Sahib and enraging many Sikhs, Singh said.
Singh alleged some "extremist elements" wanted to create discord between Hindus and Sikhs, who have been living peacefully in southern Sindh province.
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"We, like other Pakistanis, don't want a negative portrayal of our country. That was one of the reasons we didn't appear in the media. But now the situation is getting out of our control," he said.
The Pakistan Sikh Council had approached police to file an FIR but no arrest had been made so far, he said.