Akhilesh Pratap Singh and Rajdev Ranjan were killed in separate incidents in Jharkhand and Bihar respectively in less than 24 hours.
"I condemn the murders of Akhilesh Pratap Singh and Rajdev Ranjan," Bokova said.
"I call on the authorities to investigate these killings to prevent impunity for crimes against freedom of expression and freedom of information from taking root."
Ranjan, Bihar's Siwan district chief of Hindi daily 'Hindustan', was shot dead when he was going on his motorcycle near a fruit market on May 13.
His killing came less than 24 hours after Singh (35), a journalist of a news channel, was gunned down by unidentified men at Dewaria in Chatra district in Jharkhand.