Kyrgyzstan authorities Tuesday detained on corruption charges a powerbroker to former president Sooronbay Jeenbekov, as a new acting leader seeks to consolidate power with an anti-graft drive.

Ex-deputy customs chief Rayimbek Matraimov was regarded as a key financial backer for political parties and presidents, including Jeenbekov.

Jeenbekov stepped down last week in the wake of protests that followed a disputed parliamentary election on October 4, leaving power in the hands of Sadyr Japarov as prime minister and acting president.

The national security committee said that Matraimov and other officials were part of "a corruption scheme established to extract shadow income during customs administration".

The scheme had begun in 2016, when Matraimov was still in his post and had resulted in "especially large scale damage" to the state budget, it said in a statement.

Japarov had pledged to bring Matraimov to justice over claims first aired in a media report that he was at the centre of a scheme that funnelled $700 million out of the impoverished republic.

He said last week that Matraimov was connected to "90 percent of state officials".

"What to do? Allow only 10 percent to keep working?" he asked.

Matraimov was seen as the main backer of the Mekenim Kyrgyzstan party that dominated the parliamentary vote along with a party called Birimdik that included Jeenbekov's brother among its ranks.

Last year he was the target of protests led by civic groups who called on authorities to investigate the allegations in a report made by anti-graft activists.

The precise nature of Jeenbekov's relationship with Matraimov was unknown, with some observers speculating that they had fallen out towards the end of Jeenbekov's time in office.

Power is currently in the hands of prime minister and acting president Sadyr Japarov (left) after Sooronbay Jeenbekov (right) stepped down following a disputed vote
Power is currently in the hands of prime minister and acting president Sadyr Japarov (left) after Sooronbay Jeenbekov (right) stepped down following a disputed vote AFP / VYACHESLAV OSELEDKO

But Jeenbekov notably failed to push forward a criminal investigation targeting contraband and money laundering that was opened following the protests.

The publishers of the report, the Organised Crime and Corruption Reporting Project, described Matraimov as a gatekeeper for an "underground Central Asian cargo empire".

Bolot Temirov, an investigative journalist who was beaten up by a group of men not long after his fact-checking outlet published a separate report on Matraimov's wealth, told AFP that it was too early to celebrate the former official's demise.

"The new authorities need to make a good show of themselves as quickly as possible," said Temirov.

"Matraimov's arrest is a win-win option for them. But the threat remains the same. (Matraimov) has money and influence."

The Matraimov and Jeenbekov-affiliated parties were accused of massive vote-buying and the results were annulled after protests morphed into clashes between police and supporters of opposition parties.

Japarov, 51, who claimed power less than two weeks after he was sprung from jail by supporters, styled himself as a reformist in a speech on Friday one day after Jeenbekov's resignation.

The populist politician said that the fight against corruption would "cease to be a tool for eliminating political opponents", pledging that organised crime "will stop dictating its terms".

Japarov has angrily denied suggestions he has his own ties to organised crime, amid media allegations during his overnight rise to power during the post-elections crisis.

With a re-run of parliamentary elections expected in December and presidential polls by mid-January, Japarov still must work to tighten his grip on the ex-Soviet state.

There has as yet been no indication that key ally Russia recognises his new functions.

Prior to his release he was serving jail time for hostage taking -- a conviction related to an incident that took place during a 2013 rally in support of the nationalisation of a key foreign-operated gold mine.