He said March protests led to 12 deaths while Saba Saba and Wednesday's killings leading to 18 deaths.Others are yet to be tallied.
According to Houghton, most victims succumbed to targeted shootings, brutal beatings and suffocation from teargas.
"Preliminary investigations have revealed that the police have used beatings, arbitrary arrests and detention of protestors, indiscriminate and disproportionate use of tear gas and water cannons, and other serious rights violations to police the protests," said Houghton.
Amnesty has urged restrain from criminalising protests and use of excessive force against unarmed protestors.
"The Inspector General of the Police, Japhet Koome and the Cabinet Secretary of Interior and Administration of National Government, Kithure Kindiki must take practical steps to guarantee the right of everyone to peaceful assembly and protest," he said.
On the use of non-uniformed officers who conduct arbitrary arrests of protestors, he said transparency and accountability should be upheld as the acts violate the service's codes of conduct.
"Police officers must be identifiable by uniform or number badges to avoid abuse of power and other violations," he said.
Swift investigations
While calling for swift investigations from Independent Police Oversight Authority into the killings, he urged the state to uphold its "duty to protect protestors from intimidation and suppression."
He called on the government agencies tasked with promoting peace and unity-National Cohesion and Integration Commission to censor and take necessary action against leaders inciting the public.
Houghton further expressed the organisation's concern on access to essential services including healthcare by the public.