The tourists, following on 418 runs behind after being dismissed for a new low of 81 against Sri Lanka in the first innings, went to lunch on the fourth day at 102-1 in their second knock.
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Left-hander Cook was unbeaten on 53 and Ian Bell was on 17 in an unbroken stand of 35 for the second wicket.
Sri Lanka, who lead 1-0 in the series, have five sessions left -- weather permitting -- to force a 2-0 scoreline that will lift them to second place in the official Test rankings behind Australia.
Light rain forced the players off the field five minutes before the scheduled lunch break and more wet weather has been forecast over this coastal town in the next two days.
Cook, the 22-year-old Essex opener, and captain Michael Vaughan gave England a solid start by adding 67 for the first wicket.
Vaughan made a watchful 24 when a flashy stroke caused his dismissal 90 minutes after the start of play.
Vaughan attempted to drive left-arm seamer Chanaka Welegedara outside the off-stump and