Jibril Al Rajoub said that 37 sports officials and journalists had died in the beleaguered strip during the conflict between Israel and Hamas.
Al Rajoub told AFP that three of the dead were sportsmen in Gaza.
"Our participation in Incheon is a national and political battle,” he said.
"Even although the Palestinian people are living in circumstances that limit their movement inside Palestine and outside also, and financial difficulties we are facing, we were able to take part in this Asian Games with 80 sportsmen, including seven women, in 12 disciplines,” the official said.
He praised the men’s football side which has won its first two games and sits top of its group.
The Palestinians have defeated Tajikistan and Oman, 2-1 and 2-0 respectively.
"Our football team is almost through to the second round,” al Rajoub enthused. "This is a big achievement for Palestinian sports and an excellent sign of our participation.
"All our players are under 22 with no one from the first team, which has already qualified for the Asian Cup in Australia,” in January, he added.
"But I’m sure that after the good performance here, some of the players will join the Asian finals.
"I feel that we have a good improvement in football and this comes after our achievement in the AFC Challenge Cup,” which the Palestinian side won, qualifying for the Asian Cup.
The Israeli-Hamas war ended with a truce on August 26. More than 2,140 Palestinians, most of them civilians, and 73 Israelis, mostly soldiers, were killed.