The Istanbul Trump Towers complex, opened in 2012 at a cost of USD 400 million, has over 200 luxury residential apartments in the almost 40-storey landmark twin towers in the Mecidiyekoy district of Istanbul.
"We regret and condemn these discriminatory comments against Muslims," said the chief executive of Trump Towers Istanbul Bulent Kural in a statement quoted by Turkish media.
He said this position had been transmitted to the Trump family.
Trump, the frontrunner for the Republican presidential nomination, came under fire at home and abroad this week for his proposal to temporarily bar Muslims from entering the US.
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It came in the wake of last week's shooting by a Muslim couple in Sen Bernardino, California, that left 14 dead.
Kural said Trump's remarks were a "product of a mindset which never understood Islam as a religion of peace and tolerance."
He added that Trump's comments aim to "abuse our religion for small political calculations."
There are Trump Towers in several US cities and a handful of cities across the world including Mumbai and Toronto.
However the Istanbul development was the Trump Organisation's first such Towers complex in Europe. Its partner in the development is Dogan Holding, one of Turkey's biggest conglomerates with interests in energy and media.