Ambassador Basant Kumar Gupta was summoned "to express the bewilderment and profound disappointment of the Italian government", the foreign ministry said.
The move came just hours after Italy recalled its ambassador from India, Daniele Mancini, in protest over what it described as "a new and unacceptable delay by the Indian Supreme Court".
"The Indian judicial authorities' delaying tactics — two years on from the incident — are unacceptable and indicate an Indian desire to procrastinate beyond all limits," Italy's secretary general of the foreign ministry, Michele Valensise, said in a statement.
The delay in court proceedings came in spite of "authoritative stances taken by different international organisations", he said.
The two marines, Massimiliano Latorre and Salvatore Girone, who are staying at the Italian embassy in New Delhi, are accused of killing two Indian fishermen they mistook for pirates while guarding a cargo ship in 2012.
Foreign Minister Emma Bonino slammed "the evident incapacity of the Indian judicial authorities to handle this case" and said Italy "will continue and intensify action to defend its sovereign rights in line with international law."
"Italy's main aim remains trying to obtain the return of the two marines as quickly as possible," Bonino said.
An Indian Supreme Court hearing scheduled for Tuesday was immediately postponed because prosecutors are still waiting for the Indian justice ministry to decide which law to try the case under.
Attorney General Goolam Vahanvati has requested the pair be prosecuted under a maritime security law, which attracts a 10-year sentence, and on Tuesday said the matter was "under the consideration of the law ministry" and he needed "more time to work out a solution to the issue".
The next hearing will be on February 24th.
"This is too much. There is no justice in this case. We are faced with an ambiguous behaviour and a lack of trustworthiness on the part of the Indian authorities," said Mario Mauro, Italy's defence minister.
"The decision to recall the ambassador is not only justified but inevitable and reflects the feelings of the Italian people," he said.
Italian authorities have lobbied the European Union and the United Nations on the case, saying Latorre and Girone should be tried in Italy because it says the incident took place in international waters.
India denies this, saying it happened in Indian waters.
Girone's wife, Vania Ardito, told ANSA news agency that the latest delay was "an injustice".
"We are tired of waiting. Massimiliano and Salvatore are innocent and it is time they came home," she said.