Speculation about Rooney's future arose following his failure to start in United's 2-1 defeat to Real Madrid in the Champions League on Tuesday.
"There is absolutely no issue about a new contract for Wayne," Ferguson told reporters.
"When it is time to renegotiate with Wayne it will be done. We don't want our best players to leave and Wayne is coming into his mature years."
United face off against Chelsea in the quarter-finals of the FA Cup later today.