Mufti Muhammad Sayeed's pledge to try to bring the Indian Government and separatists closer has raised hopes of a new phase in the politics of Kashmir, where 30,000 people have died in a 12-year revolt.
But a series of attacks coincided with the inauguration in Srinagar, the state's summer capital, and a BBC correspondent says the separatists are clearly not impressed.
Security forces and militants were involved in the violence across the territory, which has triggered two of the three wars fought by India and Pakistan since 1947.
In Saturday's attacks:
The inauguration ceremony itself was held amid tight security at a packed auditorium in Srinagar.
Leading Indian politicians, including Congress leader Sonia Gandhi, were invited for the swearing-in of the new government - a coalition between Congress and Mr Sayeed's People's Democratic Party.
Mr Sayeed, 66, told reporters after the ceremony: "It is a historical day.
"We have challenges ahead and we have realisation but we have to work jointly. I pray to God that I come up to the expectations of the people."
He campaigned on a platform of fighting corruption, defending human rights and seeking talks between militants and central government.
The BBC's Altaf Hussain said Mr Sayeed's peace overtures were beginning to put pressure on the militants to co-operate, but Saturday's attacks have apparently shown their contempt for the prospect of making any deal.
The co-operation needed from the army and paramilitary forces - both controlled by Delhi - could also be harder to secure if the violence continues, correspondents say.
Novel agenda
The new chief minister has promised to release all militants who have no serious charges against them.
A leading militant from the Jammu and Kashmir Liberation Front (JKLF), Showkat Bakhshi, was released on Friday after 12 years in prison.
He was one of the accused in the abduction of Mr Sayeed's daughter in 1989.
Our correspondent said this novel agenda had made the separatist political leaders somewhat nervous, as the policies could have been seen as helping ordinary people - but that agenda could now hang in the balance.
Mr Sayeed will head a coalition of his People's Democratic Party and the Congress party for three years, before a Congress leader takes over for a second three-year period.