The Swiss national time-trial champion completed the 9km race against the clock around Voorburg near The Hague in 10min 58sec to push Pole Maciej Bodnar into second place by four seconds, with Giro d’Italia winner Tom Dumoulin, the Dutch time-trial champion, third at 5sec.
They are now the top three overall as Sagan finished in 18th at 25sec and dropped to eighth overall.
Four-time world time-trial champion Tony Martin of Germany finished 40sec down in 53rd after crashing on the tricky circuit in wet weather that got worse throughout the afternoon.
Kung had gone out earlier in better conditions.
Wednesday’s third stage is 185km long from Blankenberge to Ardooie in Belgium.
