While such services have become popular online communication channels, some people have used them to distribute illegal and harmful information, seriously undermining public interests and order in cyberspace, a statement from the State Internet Information Office (SIIO) said.
The campaign will target public accounts on instant messaging services, which can spread information on a large scale and mobilise followers, it said.
WeChat, China's most successful mobile based messaging service, has more than 800 million users.
Besides private accounts used for communication among friends, family and acquaintances, many public accounts are owned by organisations, companies or individuals for mass communication.
The campaign will crack down on those spreading rumours and information relating to violence, terrorism and pornography, as well as those using instant messaging for fraud, the statement said.
"We will firmly fight against infiltration from hostile forces at home and abroad," Xinhua quoted the statement as saying.
The SIIO, the Ministry of Industry and Information Technology and Ministry of Public Security are in charge of the campaign, which will hold service providers responsible if they do not fulfill their duty.
The authorities also encouraging the public to provide tip-offs through emails, phone calls or the official website.