Blatter, who went to the region two years ago to try to help improve the relationship between the Palestinians and Israel, was applauded by delegates at a conference of the Asian Football Confederation (AFC) in Mauritius before FIFA's Congress starting on Thursday.
Blatter told AFC delegates he was aware of what he called "this touchy problem", adding: "I can confirm I will help, FIFA will help. It's a problem of football. We will help you and this will be done. It's not a promise it's a will – and where there's a will there's way."
The tensions between the neighbors have been exacerbated as the start of UEFA's European Under-21 Championship, being staged in four Israeli cities next month, approaches.
Last week UEFA general secretary Gianni Infantino said after its Congress in London that European soccer's governing body was within its rights to award the tournament to Israel and would not consider moving it.
But Jibril Rajoub, president of the Palestine FA and Palestine Olympic Committee, said the situation had worsened since Blatter and International Olympic Committee (IOC) chief Jacques Rogge visited the region on separate occasions in 2011 and 2010.
At Rajoub's request there will be an open debate on the situation at the FIFA Congress on Friday.
Palestinians are angry that Israel's security forces, who control movement between Gaza and the West Bank, frequently prevent athletes from travelling freely between the two areas.
The situation is not restricted to Palestinians.
As a full member of FIFA and the AFC, the Palestine FA has started to hold more regional tournaments but the Israelis are stopping athletes from third countries entering the West Bank.
Recently two teenagers from Myanmar were stuck in Jordan for a week awaiting clearance so they could play in an Under-17 tournament before eventually been granted access to the Palestinian territories.
After Wednesday's meeting, Rajoub told Reuters: "It's crazy what the Israelis are doing. They should be asked either to respect and accept the statutes or pay the price. I am talking about free access and free movement for both athletes and sports instructors and experts from abroad.
"We just want to enjoy sport like the rest of the associations."
Asked whether IOC and FIFA intervention had helped, he said: "No. The situation is deteriorating. They have to recognize reality on the ground and Palestine is a member of both FIFA and the IOC and accepts all of the standards and statutes of FIFA."
He also objected to Israel hosting next month's Under-21 finals saying: "They should not be given this gift as long as they are not giving Palestinians the right to enjoy the same things as them."