Students Azamat Tazhayakov and Dias Kadyrbayev, both 19, were charged by US authorities with conspiring to obstruct justice by hiding a backpack and fireworks they found in the dorm room of one of the suspected bombers.
They face up to five years in prison if found guilty.
A third man, a US citizen, also 19, was charged with making false statements to investigators. "Kazakhstan strongly condemns any form of terrorism," the Foreign Ministry said on its website yesterday. It said Astana was co-operating with US law enforcement agencies on the case.
The ministry emphasised that Kadyrbayev and Tazhayakov were charged with destroying evidence and not with involvement in organising the attack on the Boston Marathon on April 15, which killed three people and injured 264.
"Their guilt has not been proven and the investigation is ongoing," the ministry said.
US court papers say three days after the blasts, the trio moved swiftly to cover up for their friend when the FBI released pictures of the suspected bombers, made a public plea for help locating them and conducted a day-long manhunt that left much of Boston on lockdown.
The students were described as college friends of surviving bomb suspect Dzhokhar Tsarnaev. At their initial court appearances on Wednesday, none of the three entered a plea. After the proceedings, an attorney for Kadyrbayev, Robert Stahl, said: "Dias Kadyrbayev absolutely denies the charges. He did not know this individual was involved in the bombing. His first inkling came much later."
Tsarnaev faces the possibility of execution if he is convicted over the blasts.