Boa Morte has joined Manchester United's Cristiano Ronaldo in Portugal's Olympic squad and Coleman knows he is powerless to prevent him from going to Greece.
The former Arsenal star could now miss four Premiership games because of his trip.
"We're going to lose Boa for a while, which is not ideal," said Coleman.
"I didn't want him to go to the Olympics but I have to accept his wishes.
"He was upset at missing out on Portugal's squad for Euro 2004 but he's been called up for the Olympics and he wants to go. There's nothing we can do about that except hope Portugal get knocked out in the first round!
"He's an important player for us - he has tremendous pace and strength and will be sorely missed."
Meanwhile, Coleman has confirmed that he wants Junichi Inamoto back at the club - but is refusing to meet his club Gamba Osaka's asking price.
Inamoto has spent the last two seasons on loan at Fulham, after spending an unsuccessful campaign with Arsenal.
Coleman has now confirmed that talks over Inamoto's future have stalled.
"Ina's club want too much money as far as I'm concerned and I'm not willing to pay that much. He has a year left on his contract," added Coleman.
"He did very well last year. He was in and out but when he was playing he did a very good job for us. He's a good squad player with a great attitude.
"He has integrated well into the changing room and is very popular among the lads. We're interested in bringing him back, but only at the right price."
