The Malaysia Home Ministry is denying that the police practiced double standard in terms of treating groups who staged different protests in March and April on which was aimed against Christians.

In a letter to a member of parliament, Home Minister Datuk Seri Ahmad Zahid Hamidi held that the investigations had been done fairly and just regardless of the personalities involved.

"Police have never practiced double standards or selective investigation in any of their investigations or action," Hamidi wrote to Lim Kit Siang, Member of Parliament for Gelang Patah, The Malaysian Insider reported.

Lim tweeted at the beginning of May asking why the police gave the protesters at Taman Medan "kid glove treatment" while those who staged an unrelated sit-in at the Customs office in March had been arrested.

The home ministry clarified that the country's constitution expressly states limits into freedoms of assembly and expression contrary to some liberal interpretations of the contested provisions.

"While the Federal Constitution allows the freedom to gather and give opinions, it also sets a limit," the ministry said. "In other words, there is no absolute freedom for anyone to freely gather and voice their views, especially since if it is against the country's laws."

On March 23, more than 100 people staged a protest at the Customs office in Kuala Lumpur to ask for answers to their queries on the department's scheduled rollout of a goods and services tax on April 1.

The protesters were led by Parti Socialis Malaysia and some of the participants came from different civil society groups.

Police broke up the sit-in, arresting 79 people after a scuffle erupted among the authorities and the protesters.

In the other protest in April, some 40 Muslim demanded that a church in Petaling Jaya remove a cross installed in the building's façade.

They said it challenged Islam, the religion adhered to by 61 per cent of Malaysia's 30 million people, and that it coerced young people to convert to Christianity.

Among the protesters was Datuk Abdullah Abu Bakar, the brother of Inspector-General of Police Tan Sri Khalid Abu Bakar. Abdullah Abu Bakar had asserted he was trying to calm the protesters down.

The home ministry said the sales tax protest had seen cases filed in the courts.

Regarding the church protest, no cases had been filed against the protesters because the investigation was still ongoing.