Pakistan summoned Brinkley on Tuesday and told him awarding a knighthood to Rushdie was insensitive and contrary to efforts to foster understanding between religions.
Rushdie, whose novel "The Satanic Verses" outraged many Muslims around the world, was awarded a knighthood for services to literature in Queen Elizabeth's birthday honours list published on Saturday.
Tasnim Aslam, the Pakistani foreign ministry spokeswoman, said Brinkley "was called in regarding the conferment of a knighthood on Salman Rushdie"
"He was told that Salman Rushdie has been a controversial figure who is known less for his literary contribution and more for his offensive and insulting writing which deeply hurts the sentiments of Muslims all over the world," she said.
"Conferment of a knighthood on Salman Rushdie shows an utter lack of sensitivity on the part of the British government," she said.
Rushdie's book prompted protests, some violent, by Muslims in many countries after it was published in 1988.
Ayatollah Ruhollah Khomeini, the late Iranian supreme leader, issued a fatwa death warrant against Rushdie in 1989, forcing him into hiding for nine years.
The Pakistani parliament adopted a resolution on Monday deploring the knighthood, and the government's religious affairs minister said the honour could incite suicide bombings.
Brinkley said on Monday Rushdie's knighthood was a reflection of his contribution to literature throughout a long and distinguished career.
"It is simply untrue that this knighthood is intended as an insult to Islam or the Prophet Muhammad," he said in a statement.
"Islam is the second largest religion in the UK and is regarded with the highest level of respect, in recognition of the important cultural and intellectual achievements of this important religion."
Aslam said the knighthood was resented and it was contrary to Pakistani and British attempts to build understanding.
"The people of Pakistan and, indeed, Muslims all over the world, resent this decision. It was not expected of the UK which itself has a large Muslim population" she said.
"The British High Commissioner was further told that Pakistan deplores and regrets this decision which is contrary to our common objective of building inter-civilisational and inter-religious understanding and harmony."
Britain's twice-yearly honours ritual, designed to recognise outstanding achievement, is part of an ancient and complex awards system.
A total of 946 honours were handed out in the birthday list, including 21 knighthoods.