Pawar, the nephew of NCP president and Union Minister Sharad Pawar, was sworn in at Raj Bhawan here.
Governor K Sankaranarayanan administered oath of office to Pawar in the presence of Chief Minister Prithviraj Chavan.
Opposition Sena-BJP members, which have denounced the move, kept away from the swearing-in ceremony.
The dramatic announcement of resignation of Pawar on September 25, in the wake of allegations of corruption in irrigation projects, had plunged the state's Congress-NCP government into a crisis with all other 19 party ministers offering to quit.
Pawar, 53, had resigned after media reports alleged he had arbitrarily awarded irrigation contracts worth over Rs 20,000 crore when he was state's irrigation minister during 1999-2009, before he was elevated as deputy chief minister and handled the plum finance and energy portfolios.
The white paper, presented by the irrigation department to the state Cabinet on November 29, had claimed a 28 per cent increase in irrigation potential in Maharashtra in the last ten years.
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It was described as a status paper on irrigation and not an investigation report.
Chavan had announced a white paper on irrigation would be brought after state's economic survey report said the state's irrigation potential had risen only by 0.1 per cent between 2001 and 2010.
All these years the irrigation portfolio was with the NCP. MORE