25 people were killed and 70 injured when the Yamaguchi-gumi split in 1984
The arrests are intended to deplete manpower and funds from the Yamaguchi-gumi, the nation's largest crime syndicate, and the Kobe Yamaguchi-gumi, which broke away in August last year.
A worrying precedent for such a breakaway was set in 1984, when 25 people were killed and 70 others injured in bloody clashes between rival gangs.
Japanese police set up a dedicated unit to "intensify" their response to the group's split and began conducting a series of raids and arrests.
Since the country's National Police Agency announced the gangs were in a "state of all-out war" on 7 March, they have arrested 976 gangsters, often over minor infractions, The Asahi Shimbun reports.
“After the split, the police have been relentlessly arresting members even for spontaneous scuffles or damage to property,” a gangster allegedly affiliated with the Yamaguchi-gumi told the paper.
“Every time someone gets arrested, we have to pay for a lawyer. It is a horribly exhausting battle.”
Of those arrested, 623 were members of the Yamaguchi-gumi and 353 were from Kobe Yamaguchi-gumi.
The gangs allegedly engage in a range of activities, including gambling, drugs, prostitution, loan-shark operations and protection rackets.
The split occurred when five subsidiaries of the Yamaguchi-gumi were expelled from the group and eight others suspended.
The subsidiaries were exiled for voicing concern with gang-boss Shinobu Tsukasa's management after they criticised him for failing to focus the organisation's operation on the more lucrative Tokyo market. The gang operates predominantly in western Japan.
Following failed negotiations between the two gangs, Tadashi Takagi, a senior member of the Koba Yamaguchi-gumi, was shot and killed on 31 May and Tatsuo Saiki, another member of the gang, was shot dead on 15 July.
There have also been reports of trucks being crashed into offices belonging to the rival groups.