"I look back and express deep regret and repentance over how the Netherlands dealt with human values," he said at the ceremony, which King Willem-Alexander and Queen Maxima attended.
Many Dutch Surinamese were angry the minister did not issue an outright apology to the victims of slavery, DutchNews.nl said.
They were also unhappy the royal couple did not lay a wreath on the slavery monument, which was unveiled by the king's mother, Beatrix, in 2002.
Amsterdam Mayor Eberhard van der Laan also spoke at the ceremony.
"This history fills us with shame," the mayor said.
Slavery was banned in the former Dutch colony of Suriname and on the Caribbean Antillean Islands in 1863, 150 years ago.
The Netherlands was one of the last western countries to abolish slavery.