The previous mark of 12:39.36 was set by fellow Ethiopian Haile Gebrselassie in Helsinki on June 13, 1998.
"It was very difficult," Bekele told Dutch
"The pace was a little slow (at the beginning)."
Bekele, the world 10,000 metres champion, beat Gebrselassie over that distance at last August's Paris world championships.
He will contest the 10,000 metres event at a meeting in Ostrava, Czech Republic, on June 8.
"I haven't decided what to run at the Olympics and the results will help me determine that," the Ethiopian said earlier this year.