Erdogan told Al Jazeera in an interview recorded earlier on Saturday in Istanbul: "This is not designed to isolate any country. It should not be taken from this (point of view)."
Musharraf has toured the Middle East and Asia recently to garner support for a Muslim initiative to stem the deepening conflicts that are destabilising parts of the Islamic world.
The foreign ministers of Egypt, Indonesia, Malaysia, Turkey, Jordan and Saudi Arabia will gather in Islamabad to lay the groundwork for a summit of Muslim leaders at an unspecified date in the holy city of Mecca, Saudi Arabia.
The Pakistani foreign minister said in a statement that the goal of the summit is "a new initiative to address the grave situation in the Middle East, in particular the Palestinian issue, and for harmony in the Islamic world".
Musharraf has visited Saudi Arabia, Egypt, Indonesia, Malaysia, Turkey and Iran in the last few weeks to seek common ground for his initiative.
He did not invite Iran or Syria for the meeting in Islamabad on Sunday.
Erdogan said Iran and Syria will be invited in a later stage.
Tasnim Aslan, Pakistan's foreign ministry spokeswoman, also denied the conference aims at forming a Sunni alliance.
Aslan told Al Jazeera: "It is not for Sunni countries, they are Islamic countries."
Khursheed Kasuri, Pakistan's foreign minister, said earlier this month that conflicts in the Muslim world were fostering Islamic extremism.
Musharraf said he was trying to gather countries who support "a conciliatory approach instead of a confrontationist approach" to the region's problems.