Pakistan's top spy agency, the Inter-Services Intelligence (ISI), and the army have been quietly deployed in Karachi to uproot the dominant political force from the country's most populous and largest city.

The move is seen as an attempt by the military to wade into the civil sphere to displace the Muttahida Qaumi Movement (MQM).

"There is a quiet, creeping takeover of Karachi by the military. Karachi is just too big ... too much land, too much business, resources. No one party will be allowed to rule Karachi from now on," a government official, who works in close proximity with ISI chief Rizwan Akhtar, told Reuters.

Dubbed by critics as "mission creep", the operation was widely believed to have been started in 2013 against the MQM, the political party which has long dominated the commercial hub.

The party, led by exiled leader Altaf Hussein who lives in the UK, is the fourth biggest force in the national political landscape and the dominant force in Karachi. It has seats in both the national assembly and the Sindh provincial assembly.

Hussein fled Pakistan in 1991 fearing murder charges in his home country and is currently on bail over money-laundering allegations in Britain.

Only a week ago, five activists who work for the MQM were sentenced to 25 years in prison by an anti-terrorism court for attacking security personnel. This came after raids in March, during which paramilitary rangers seized a huge cache of arms from the party's headquarters in Azizabad. The MQM denied the allegations and said they were politically motivated.

Although Pakistan's law enforcement agencies insist criminals and militants are the real targets, the operation is seen as anti-MQM.

"What is happening now [raids and arrests] is inconceivable to us. But they will not be able to dismantle the party, if that is the plan," said MQM leader Haider Abbas Rizvi, according to Reuters.

The party won a major by-election last week by securing over 95,000 votes while the runner-up managed just 25,000 votes.