Ahmet Davutoglu, Turkey's foreign minister who is visiting Paris, said that al-Bashir would not be excluded as a delegate to the economic summit of the OIC, which groups 57 Muslim nations.
"We must approach the situation in the correct light," he said.
"It's not an invitation from Turkey, which is hosting an international meeting, and invitations are issued by the OIC."
Davutoglu said he had received no complaints about al-Bashir's plans during his trip to the French capital, where he met Bernard Kouchner, his French counterpart.
The International Criminal Court (ICC) issued a warrant for al-Bashir's arrest in March.
The warrant, the court's first against a sitting head of state, is for war crimes and crimes against humanity during the conflict in Sudan's Darfur region.
Turkey has not signed the Rome Statute which set up the ICC and has said previously the warrant could hurt moves to end the conflict in Darfur, where the UN estimates that up to 300,000 people have died since 2003.
Al-Bashir stayed away from a conference last month in Nigeria, which has signed the ICC treaty, after rights groups urged the Nigerian government to arrest him if he turned up.
Human Rights Watch also called on Turkey on Friday to either bar al-Bashir or arrest him when he sets foot in Istanbul.
"Turkey's international image will plummet if it welcomes a man wanted to answer for some of the most heinous abuses against civilians in the world today," said Elise Keppler, a senior counsel in the group's international justice programme.
The EU expects Ankara to align itself to the bloc's foreign policy as part of its accession process and has made demands for Turkey to sign the ICC treaty.
Ankara's efforts to build closer ties in the Muslim world, including countries such as Iran, Sudan and Syria, that are at odds with the West, have led some analysts to conclude that Turkey, a Nato member, is turning towards the East.
Recep Tayyip Erdogan, the Turkish prime minister, brushed aside the view earlier this week, saying that Turkey remains "anchored" to Europe while seeking equally closer ties with the Muslim world.