The party said "India is in the throes of a violent clash" between advocates of freedom of speech and the government of Prime Minister Narendra Modi is determined to "silence dissent and throttle democracy".
It also said gagging media and often subjecting them through torture is often a sign of dictatorial regimes.
"The shocking murder of senior journalist and activist Gauri Lankesh is a grim reminder of the times we live in. This mindless and cowardly assassination has not only shaken our conscience but is also an extremely sad moment for our democracy," said Congress spokesperson Abhishek Manu Singhvi.
The party said it stands as one with the rationalists, thinkers, journalists and the media fraternity.
"Congress President Sonia Gandhi and Vice President Rahul Gandhi have spoken to the Chief Minister of Karnataka Siddaramaiah and urged him to swiftly bring the culprits to the book.
"Every possible measure should be taken to maintain a safe and secure atmosphere in the state," he added.
He also said the state has put its best investigative officers to work and the chief minister has promised that the assailants will be swiftly nabbed.
"We urge the Karnataka government to take prompt action and bring these criminals to book," Mr Singhvi added.
"The series of killings of rationalists, free thinkers and journalists has created an atmosphere that dissent, ideological differences and divergence of views can endanger our lives.
"There is a definite pattern in the murder of rationalists and free thinkers and those who question the government - Dabholkar, Pansare and Kalburgi and now Lankesh," said Mr Singhvi.
He further said: "An unprecedented atmosphere of hate and intolerance is being created in order to take on those who have ideologically divergent views. 'If you do not agree with us, we shall kill you' is the new slogan of 'New India'.
Muzzling the voice of ordinary citizens and the lynch mob mentality has become a regular habit of this 'New India-Achhe Din' government, he added.
"Why is Narendra Modi following such accounts who are involved in these illegal and unlawful activities?" asked Mr Singhvi.