Ms Yousafzai, 20, was shot in the head by a gunman for campaigning for female education in 2012.
Her family's home region of Swat was once a militant stronghold.
Roads leading to Ms Yousafzai's home in the town of Mingora have been blocked off, Reuters news agency reports.
On Thursday, it was announced that she had returned from the UK to Pakistan for the first time since she was shot.
Ms Yousafzai delivered an emotional speech at the prime minister's office in Islamabad:
"Always it has been my dream that I should go to Pakistan and there, in peace and without any fear, I can move on streets, I can meet people, I can talk to people.
"And I think that it's my old home again... so it is actually happening, and I am grateful to all of you."
Her trip to Pakistan is expected to last four days. Officials from her Malala Fund group are travelling with her, local media report.
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