The head of the sport's governing body was due to meet Israel's football chiefs on Monday and was also hoping to speak to political leaders on the matter.
Palestinians are angry that Israel's security forces, who control movement between the Gaza Strip and the Israeli-occupied West Bank frequently prevent athletes from travelling freely between the two separated territories.
"I will go to defend not only the Palestine Football Association but I will defend the basic principles of FIFA (which are) to connect people and not to separate people... The principles are ... to recognise each other through football and to live not only in peace but in harmony," Blatter said.
Palestine FA head Jibril Rajoub threatened that if the matter was not resolved satisfactorily, he would call on delegates at the next FIFA Congress to expel Israel.
Israel cites security concerns but says it has eased travel for athletes between Palestinian territories. The Palestinians want the West Bank and the Gaza Strip for a future state with Arab East Jerusalem as its capital.
The West Bank, which is controlled by Western-backed Palestinian President Mahmoud Abbas of the secular Fatah faction has self-rule in some areas but Israel has overall military control of the territory.
The Gaza Strip, from which militants have fired thousands of rockets and mortar bombs into the Jewish state in recent years, is ruled by the Islamist Hamas faction which calls for Israel's destruction.
Israel allows a small number of Palestinians through the border posts that it controls around Gaza, mainly for medical treatment. It also maintains a naval blockade of the strip but a border crossing with Egypt is largely open for travel.
"We hope the Israelis will not lose this chance to reconsider their behaviour with the Palestinians. If they do not ... we will ask next year that Israel should be expelled from FIFA," Rajoub said.
Blatter came to the West Bank from Jordan and attended a number of ceremonial events at various locations, including opening new offices for the Palestine Football Association near Ramallah, the Palestinian seat of government.
Blatter said that the Palestine FA would bid to host the FIFA Congress in 2016 or the following year.
- Palestinian territories