Ferguson underwent emergency surgery at Salford Royal Hospital on Saturday and remains in intensive care.
Speaking ahead of United's trip to West Ham United on Thursday, Mourinho refused to reveal whether he had visited Ferguson in hospital, instead reiterating the family's request for privacy.
Sir Alex Ferguson - A career in pictures
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Yet when asked whether Ferguson's condition would cast a cloud over the end of the club's season, Mourinho said: "We are positive, we are very, very positive. We are confident."
The United manager also denied that events of the last week would affect his players, claiming: "I can only think that if there is any relation it is a positive relation."
Ferguson is the most successful manager in Manchester United's history, winning 13 Premier League titles and two European Cups alongside a host of other trophies during his 27 years in charge.
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