They also submitted identical petitions to President Pranab Mukherjee and Prime Minister Manmohan Singh requesting them to look into the matter.
"Through this petition, we urge you to do everything in your authority and influence to clear Prof. Chakrabarti and appoint him as the next director of IIT-Kharagpur without any further delays and before July 29," they pleaded.
IIT-Kharagpur is the oldest among the 17 Indian Institutes of Technology in the country. Of the 17, nine have come up after 2008.
Alumni, teachers and students held protests in Kolkata, Delhi and Bangalore to seek 48-year-old Chakrabarti's appointment as the institute's head.
In Kolkata, over 200 faculty members and alumni participated in a silent protest. Professors and alumni members gathered at Allen Park in Park Street in the heart of the city to put across their point via placards and banners.
"We will carry on our protests till Chakrabarti is appointed," Rajendra Singh, general secretary of the association, told IANS.
Although the acting director has been discharging the directorial duties, Singh said a full-time head was necessary for executing long-term plans, including execution of the institute's 'Vision 2020' charter that envisages making IIT-KGP one of the top 20 institutes in the world.
The protest in Delhi, led by IIT-KGP alumni association, started amid continuous rain with marchers claiming that the Kharagpur institute, around 135 km from Kolkata, had suffered without a director for almost a year.
Members of the IIT Alumni Foundation have been pressing for having Chakrabarti as the director, a process that has been stalled for over a year due to an alleged delay by the Central Vigilance Commission (CVC) in clearing his name.
The post of the director of the institute has been vacant since June 30, 2012.
"It is unfair that PPC (Chakrabarti) has not been appointed as the director, he is the most deserving candidate," said S.M. Murmo, a member of IIT Kharagpur alumni association.
Protesters raised slogans in favour of Chakrabarti, and displayed placards that read "Save IIT Kharagpur", "CVC, MHRD, clear PPC now", "IIT Kharagpur, no director for one year" and "PPC for director".
Chakrabarti's appointment as director was halted as he was accused in the Coal Net case between IIT and Coal India Limited (CIL), which was probed by the Central Bureau Investigation (CBI) and Central Vigilance Commission (CVC).
Coal Net was a Rs.28-crore project that would enable data sharing between the coal ministry and CIL and its subsidiaries. It was awarded to IIT-Kharagpur.
However, against the rules, the institute awarded the project to a third, private party, owned by an alumnus. IIT-Kharagpur's, alumnus and co-founder of Hindustan Computers Ltd (HCL) Arjun Malhotra claimed in Delhi Friday that the CBI report recommended only a minor penalty against Chakrabarti.
According to CVC guidelines, matters with minor penalty must be resolved within two months of receiving statements. Alumni members say Chakrabarti had responded to the first CVC/CBI enquiry over four-and-a-half years ago.
In tech hub Bangalore, about 100-odd alumnus took out a rally urging the central government to appoint Chakrabarti.
"As the union human resource department (HRD) ministry has not appointed Chakrabarti as director, we are forced to protest the delay as we are former students of the renowned institute and concerned," IIT-KGP Alumni Association (Bangalore chapter) president Utkal Mohanty told IANS.
Chakrabarti, an alumni of the institute, was selected by the ministry's search-cum-selection committee July 29, 2012 for the director's post for the next five years after Damodar Acharya retired in June last year.
The first Indian Institute of Technology was born in May 1950 in Hijli, Kharagpur in a British era detention camp. It is possibly one of the very few institutions all over the world which started life in a prison house.
From a modest start in 1950, IIT-Kharagpur has been engaged in a steady process of development with about 18 academic departments, five centres of excellence. The vast tree-laden campus, spreading over 2,100 acres has a self-contained township of over 15,000 inhabitants.