The three Islamabad-based European ambassadors were summoned to the Foreign Office to receive a strong protest, the Ministry of Foreign Affairs said on Friday.
"This is an act of discrimination," junior Foreign Affairs Minister Makhdum Khusro Bakhtiar told Pakistan's parliament shortly before it passed a resolution calling the incident inappropriate.
An eight-member delegation from the Senate, parliament's upper house, arrived in Brussels on Tuesday for talks on Kashmir and other issues with the Foreign Affairs Committee of the European Parliament, Pakistani media reported.
But security staff at Brussels airport stopped the cleric, Senator Maulana Sami-ul-Haq, saying he needed clearance from the Belgian Interior Ministry to enter the country, the state-run Associated Press of Pakistan reported.
Haq is a senior leader of an alliance of Muslim parties, a strong force in Pakistan's national parliament and two conservative states neighbouring Afghanistan that opposed the US-led war that toppled the former Taliban rulers in Kabul in 2001.
Other members of the delegation were not stopped and Haq was allowed to join them after a 90-minute delay.
"This is an act of discrimination"
Makhdum Khusro Bakhtiar,
Pakistan's junior Foreign Affairs Minister
Pakistani embassy officials informed the delegation on Wednesday that the Foreign Affairs Committee was only willing to meet the delegation if Haq was not included, but the senators refused.
Haq runs the Darul Uloom-e-Haqqania, a major Muslim religious school in Pakistan where several prominent Taliban members studied.
The ambassador of the Netherlands was summoned to receive the protest over the affair because that country represents in Pakistan the interests of Luxembourg, the current president of the EU.