The Kenyan government on Friday condemned the vandalism and looting of a national fertiliser depot during this week's deadly protests, saying it threatens a "catastrophic" food production crisis.

Thousands took to the streets across Kenya on Wednesday to mark one year since massive anti-tax demonstrations.

The rallies began peacefully but descended into chaos as young men battled police and destroyed thousands of businesses, leaving 16 dead and hundreds injured, according to rights groups.

The ministry of agriculture said in a statement that more than 7,354 bags of fertiliser, worth around $230,000, were looted from a national depot in Meru, about 200 kilometres (120 miles) east of Nairobi.

"Fertiliser was looted, fertiliser meant to sustain farmers through this planting season," the ministry said, calling it "a direct assault on Kenya's food security".

"Its loss threatens to trigger a catastrophic crisis for both food crop and cash crop production."

Meru is one of Kenya's leading agricultural counties, contributing to a sector that accounts for about 21 percent of GDP.

Agriculture minister Mutahi Kagwe called for the arrest and prosecution of those responsible.

Kipchumba Murkomen, Kenya's interior minister, on Thursday condemned the protests as "terrorism disguised as dissent" and backed the police's use of force.

The United Nations deplored the violence and called for calm, restraint and an investigation.