NAIROBI, Sept 24 (Reuters) - Weapons discovered by Kenyan authorities aboard a Norwegian ship were part of a legitimate cargo for United Nations peacekeepers and the vessel should not have been inspected without a U.N. presence, a U.N. spokesman said on Thursday.

Kenyan authorities said they uncovered weapons and a drug-like substance stashed inside a shipment of U.N. vehicles when they boarded the Norwegian-flagged Hoegh Transporter at the port of Mombasa last week.

"It is unfortunate that the Kenyan authorities inspected the cargo without a U.N. presence, which runs contrary to established protocol and provisions surrounding privileges and immunities," the U.N. said in a statement signed by its spokesman in Nairobi, Nasser Ega-Musa.

"We are also aware of the disturbing allegations that drugs were also found on the vessel. This is being currently investigated by the responsible authorities," he said.

Coastguards and navies in East Africa have struggled to stem the flow of drugs through their waters as the region has become a key export route for Afghan heroin destined for Europe.

The U.N. statement said the weapons found aboard were part of a legitimate cargo of armoured personnel carriers destined for the Indian battalion of the U.N.'s peacekeeping mission in the Democratic Republic of the Congo, the statement said.

"It is normal practice for weapons attached to the APCs to be dismantled and placed inside the carriers in order to avoid damage whilst being shipped," it added.

The contractor responsible for the shipment had provided additional information on the arms to Kenyan port officials, the U.N. said, adding it was co-operating fully with them.

Hoegh Autoliners, the Norwegian owner of the vessel, said on Wednesday the weapons found aboard had not been declared by the shipper and their presence violated the terms of the shipping agreement.

Francis Wanjohi, the regional police commander responsible for Mombasa, told Reuters on Thursday investigations were not yet complete.

(Reporting by Duncan Miriri; Editing by Mark Trevelyan)