Patriarch Irinej said the Church's first duty was to help recover the breakaway province.
The 80-year-old is considered a moderate who is open to modernisation.
He has said he would not be opposed to Pope Benedict XVI visiting Serbia, suggesting a possible rapprochement with the Roman Catholic Church.
The service in Belgrade was the first part of a two-stage induction process, with a second ceremony due at Pec in western Kosovo.
"Our first duty as a Church is to safeguard our Kosovo, a holy and martyred land, to help our state to defend it from those who wish to seize it," Patriarch Irinej said in a speech after his enthronement on Saturday.
"Kosovo is our holy land, our Jerusalem," he added. "We must go to Pec to complete this ceremony, but can we visit our relics?
"Without them, Serbia is not Serbia, without Kosovo it is deprived of its heart and soul."
Kosovo unilaterally declared independence from Serbia in February 2008.
The Serbian Orthodox Church has about 11 million members worldwide.
Most of Serbia's seven million people are Orthodox Christians.
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