Additional Session Judge V G Sreedevi also allowed the prosecution petition to list two other CPI(M) leaders, including Idukki District Secretary K K Jayachandran as accused in the case.
Mani, a party state secretariat member, is the second accused in the case.
The case was reopened by the previous Congress led UDF government after Mani made two controversial speeches in 2012 in which he publicly stated that the Communist party had often eliminated its political foes in Idukki district in the 1980s.
The youth leader, Anchery Baby was shot dead at Udumbanchola in the district on November 13, in 1982.
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There were nine accused in the case and were acquitted by a lower court, which was later upheld by the High Court.
Reacting to the court order, Mani said the case was politically motivated.
"The verdict is not going to effect me in any way", he said while rejecting the demand for his resignation from the Congress and BJP.
Mani was inducted as Minister last month after the resignation of then Industries Minister E P Jayarajan in the wake of allegation of nepotism in appointments in PSUs.
"He should resign on his own or Chief Minister Pinarayi Vijayan should oust him from the cabinet," Sudheeran said.
(REOPEN LGM1)
Meanwhile Mani told reporters in Kottayam that he would fight the case politically and legally.
"It is a politically motivated case. I will fight the case both legally and politically. An appeal against the verdict will be filed in the higher court soon," he said.
To demands from the opposition parties, led by leader of the opposition Ramesh Chennithala for his resignation, Mani said it was not possible for him to resign when they raise such demands.
Mani, a party state secretariat member, is the second accused in the case.
Chennithala described as "unfortunate" Mani's statement that he would not quit office in wake of the court ruling and urged the Chief Minister to oust him from the Cabinet.
"Mani has no moral right to continue in office. It is very unfortunate that a person holding high office of a state as a minister is refusing to quit even after a court rejected his plea to quash the murder case against him," the Congress leader told reporters in Kochi.
BJP also demanded the immediate resignation of Mani, saying the minister does not have the right to remain in office following the court verdict.
"Mani does not have the right to continue as minister even for a minute", BJP state president Kummanam Rajasekharan said in a statement.
He recalled that leaders like K Karunakaran,R Balakrishna Pillai and K M Mani had resigned in similar circumstanes
Former Union minister O Rajagopal said Mani should resign immediately or the ChiefMinister should seek his resignation.