Manchester United captain Wayne Rooney has been left out of the squad for the Europa league tie at FC Midtjylland on Thursday amid fears he could be out for as long as two months due to a knee ligament injury.
The England forward Rooney did not travel to Denmark for the last-32 first-leg match.
Van Gaal explained Rooney's absence during a media conference.
Sky Sports claim Rooney is expected to miss six weeks, but Van Gaal said he did not know how long his captain will take to recover from the blow.
A two-month absence would see the 30-year-old Rooney miss up to 11 matches with United and two with England, but a six-week recovery period would still be a serious setback for Van Gaal and United.
"We have 13 players injured and Wayne Rooney is one of them," said Van Gaal.
"He scores a lot of goals so he is very important for us. We know that but we have to cope."
Rooney has scored seven goals in his past nine appearances for United. He is United's top scorer with 14 goals in all competitions.
United occupy fifth place in the Premier League, six points adrift of fourth-placed Manchester City with 12 matches remaining.
Van Gaal said after Saturday's 2-1 loss at Sunderland that winning the Europa League was looking the most viable route into the Champions League.
Rooney's injury is not only a concern to United's hopes of finishing in the Premier League top four with national coach Roy Hodgson preparing for the Euro 2016 finals in France in June.
England face international friendlies next month against Germany and the Netherlands. He has been blighted in previous years by injury preparing for major tournaments with England.
He broke a metatarsal before the World Cup finals a decade ago, and toiled with an ankle injury before the 2010 finals in South Africa.
Hodgson said on Saturday that Rooney – England's all-time record goalscorer – will be ''a player we need to depend upon'' in France.
Rooney has netted three times in four outings for England this season.
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