In the three weeks since the deadliest attack yet by al-Shabaab Islamist militants on Kenyan soil, authorities in Nairobi have frozen bank accounts of 86 Muslim entities, stopped the local operations of Somali money transfer companies and threatened to oust 350,000 refugees.
But there are signs that its heavy-handed crackdown has backfired. "The very same people who are crucial to co-operation over counter-terrorism are being targeted," says Khelef Khalifa, chairman at Muslims for Human Rights (Muhuri), whose office was raided last week.
"We have been treated like second-class citizens - the whole community has been condemned as terrorists," he says. "Every time you want to co-operate with the government they treat us like an enemy; it is very difficult for any Muslim now."
His comments get to the heart of the dilemma Nairobi faces. Authorities there believe Kenyans led and financed the jihadi massacre that targeted Christians and claimed 148 lives at Garissa university on April 2, bringing to 400 the number of people killed in Kenya by Shabaab in the past two years.
While the al-Qaeda linked group is headquartered in neighbouring Somalia, it increasingly targets Kenya and relies on Kenyan membership. Some 5m Somalis live in Kenya. In an attempt to stem terrorism that President Uhuru Kenyatta says is "deeply embedded in our communities", Nairobi is now focusing on radicalisation at home
Mr Khalifa's organisation, which draws funding from western donors, is among those the government listed this month as associated with al-Shabaab, claims he denies. The group, which regularly accuses the police of abusing Muslims' rights, argues that marginalisation of Muslims is among the chief causes of radicalisation. He says recruitment by al-Shabaab of Kenyan youth is increasing directly as a result of government policies.
This month, armed security officials raided the offices of two human rights groups that regularly defend Muslims, including Muhuri, seizing hard drives, documents and tax records days after the government froze their bank accounts.
Armed Kenyan officials also raided the offices of HAKI Africa, another rights group that says it has documented the death or disappearance of 51 Muslim Kenyans at the hands of security officials in recent years. It too is accused of being an associate of al-Shabaab, claims it denies.
"If you truly want to fight terrorism you have to come together; you can't have civil society and government on opposing sides," said Hussein Khalid, executive director at HAKI Africa, as armed officers raided his building. He says his organisation is targeted because of its outspoken criticism of the government rather than links to radicals.
Matt Bryden, an al-Shabaab expert based in Kenya, says the government needs "a more sophisticated and calibrated set of responses" if it is to stem the appeal of violent Islamism.
He says that while some faith-based organisations in Kenya may be vulnerable to exploitation by religious extremists, the Kenyan government should strike at individual extremists rather than entire institutions.
"Al-Shabaab no longer has a clearly Somali identity ... this is now a Kenyan problem," says Mr Bryden, adding that more than 1,000 Kenyan Muslims are thought to have crossed to Somalia to join the group in the past eight years.
"Recognising the domestic threat is the first realisation, but now the government is grappling with what to do about it. If it is mishandled it could pose an existential threat to Kenya."
Mr Kenyatta has spoken of the need for a "holistic" approach to counter-terrorism, including an amnesty for ex-fighters. In his latest speech, he describes al-Shabaab's aim to "create an Islamic Caliphate in east Africa" as a threat "to the stability of Kenya as a modern democratic and secular state".
Radicalisation in Kenya has surged in recent years as Kenyan jihadis return from battlefield defeats in Somalia. But the appeal of violent Islamism also has long roots in Kenya. I
n the 1990s, many Kenyan Muslims supported the now-banned Islamic Party of Kenya. Some of the initial ideology for al-Shabaab, which grew out of the youth wing of the Islamic Courts Union in Somalia in the mid-2000s, was incubated in Kenya.
Many Muslim groups also cite a host of historic injustices over land and ethnicity as well as religious identity. "There is fertile ground [for radicalisation] here," says Mr Bryden. "Kenya's challenge is to find the long middle ground between knee-jerk reaction and the long-term systemic reforms needed in policing and administration that are years away."
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