The conservative-dominated 290-seat chamber voted 171-70 against the candidacy of Fakhroddin Ahamadi Danesh Ashtiani. There were 257 lawmakers in attendance and 16 abstained from voting.
Before the vote Ashtiani called himself an "independent" figure and promised to appoint new faces as his deputies in the ministry , opposing lawmakers accused Ashtiani of having close relations with reformists and said they will no longer tolerate such tendencies in such a crucial position.
In October the parliament rejected Mahmoud Nili Ahmadabadi, another nominee for the same post; the same body dismissed former-Science Minister Reza Faraji Dana in August over similar allegations.
The vote is an indication of the increasing rift between the moderate president and his hard-line opponents in parliament who are angry over Rouhani's decision to give ground to pro-western voices and reformists in the universities.
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Rouhani has repeatedly called for more academic freedom in Iran's universities, saying such restrictions stifle innovation and breed group-think.
The president, a relative moderate cleric elected last year, has promised to promote greater openness in the Islamic republic, but has run into fierce resistance from hard-liners in the government.