On Tuesday, armed Armenian forces killed five Azerbaijani soldiers in the disputed Nagorno-Karabakh region, RIA Novosti reported.
"Presumably, some states patronizing Armenia were unhappy with the U.S. state secretary's visit and they organized that incident," Azerbaijani Deputy Prime Minister Ali Gasanov said Friday.
Clinton visited Azerbaijan, Georgia and Armenia earlier this week.
The conflict between Armenia and Azerbaijan began in the 1980s when Nagorno-Karabakh, a region in Azerbaijan with a predominantly ethnic Armenian population, declared independence from Azerbaijan.
Both sides have gone to war over the territory and more than 30,000 people have died in the conflict.
Clinton condemned the border clashes, saying that "the use of force will not resolve the Nagorno-Karabakh conflict."
Azerbaijan and Armenian officials have agreed to talk regarding Nagorno-Karabakh on June 18 in Paris.