Japan's Prime Minister Fumio Kishida ordered on Monday a government probe into the Unification Church, after the assassination of former premier Shinzo Abe renewed scrutiny of the sect.

The group has been in the spotlight because the man accused of killing Abe was reportedly motivated by resentment against the church, which has been accused of pressuring members to make hefty donations.

Officially known as the Family Federation for World Peace and Unification, the sect was founded in Korea by Sun Myung Moon and its members are sometimes called "Moonies".

The church has denied wrongdoing, but a parade of former members have gone public with criticism of its practices, and revelations about the organisation's links with top politicians have helped tank Kishida's approval ratings.

Kishida "instructed me to use our right to probe the Unification Church", Keiko Nagaoka, minister for education, culture, sports, science and technology, told reporters.

"I will begin immediately," she said.

Kishida is expected to speak about the matter later Monday, but local media said the probe would examine whether the church had harmed public welfare or committed acts at odds with its status as a religious group.

The investigation could lead to a dissolution order under the religious corporations law, which would see the church lose its status as a tax-exempt religious organisation, though it could still continue to operate.

Only two religious groups in Japan have ever received such an order, according to local media, one of which was the Aum Shinrikyo cult that carried out the 1995 sarin attack on the Tokyo metro.

The other is a group that defrauded members.

But the government is reportedly hesitant about the possibility of issuing the Unification Church such an order due to religious freedom concerns.