The 24-year-old is set to sign a three-year contract to join Vitesse from recently-relegated J.League club Ventforet Kofu.
Havenaar, whose father Dido was a goalkeeper for ADO Den Haag in the 1980s before moving to Japan, is due to arrive in Holland early in the new year to strengthen a strikeforce that is set to be without Bony Wilfried in January.
Wilfried is due to join Ivory Coast for their African Nations Cup campaign next month.
"We have been watching him for six months and we have been impressed," Vitesse technical director Ted van Leeuwen told www.vi.nl.
"We were the first club to track him and were the first to show a concrete interest.
"That said, Mike also really wanted to come to Vitesse."
Havenaar, a 6ft 4in frontman, made his Japan debut in September and has scored twice in five appearances for the Blue Samurai.
"He is a different type of striker to what we are accustomed to in Holland," Van Leeuwen added.
"He is due to join us in early January."