The 19-year-old singer was expected to hit the stage at the O2 Arena at 8.30pm and was a booed by fans after he arrived late, reported Metro online.
A spokesperson for the O2 Arena posted an apology on a social-networking site, but failed to give a reason for the singer's tardiness.
A post on the venue's official Twitter page at 10.36pm stated, "Justin Bieber is now on stage and apologises for the lateness of his show."
The O2 representative later added, "Sorry to all the Justin Bieber fans for the lateness of his show tonight. The Tube (underground train) will still be running when the show finishes."
The concert follows a miserable 19th birthday weekend for Bieber which was marred by what he called "overly aggressive dummies".