Officiating Foreign Secretary Anil Wadhwa summoned Pakistan High Commissioner Abdul Basit to South Block and conveyed India's unhappiness over the order in strong words.
Wadhwa is officiating as the Foreign Secretary in absence of S Jaishankar, who is travelling with the prime minister.
The matter was also "raised at high levels" in Pakistan through Indian High Commission, official sources said.
Blaming Pakistan for the Islamabad high court order to release Lakhvi, Minister of State for Home Kiren Rijiju told reporters that Islamabad did not produce the evidence against him despite having enough of it.
"Pakistan did not present the evidence before the court... The way the case has been handled by Pakistani agencies. Our concern is Pakistan should deal with terrorists in a manner in which the whole global community is looking at," Rijiju said, adding "There is no bad or good terrorists, a fact which has been globally accepted".
India's reaction came within hours of the Islamabad high court declaring as void the detention order of the LeT operations commander Lakhvi, who was also the 2008 Mumbai terror attack mastermind, and ordering his immediate release.
A home ministry spokesperson said the overwhelming evidence against Lakhvi regarding his role in the criminal conspiracy leading to the Mumbai attack had not been properly presented in the court by Pakistani agencies.
"This should be ensured without delay," the spokesperson said.
Lakhvi and six others -- Abdul Wajid, Mazhar Iqbal, Hamad Amin Sadiq, Shahid Jameel Riaz, Jamil Ahmed and Younis Anjum -- have been charged with planning and executing the Mumbai attacks in November, 2008 that left 166 people dead.
India has been raising its concerns over the delay in convicting perpetrators of Mumbai terror attacks. The issue was raised by Foreign Secretary Jaishankar during his meeting with his Pakistan counterpart Aizaz Ahmad Chaudhry in Islamabad recently.