That is explained in the Doctor Who Adventure games, since their stories are canon. 'City of the Daleks'BloodyThor said:Is no one going to talk about how the hell did the doctor end up on skaro at the beginning of the show? I've read multiple reviews about this episode and some mention skaro but nothing else afterwards. SKARO WAS DESTROYED IN THE TIME WAR!!! therefore it is time locked, therefore the doctor cannot enter and land on skaro! i mean yes dalek khan did it but he lost his mind afterwards in the episodes when David Tennant was still the doctor (and the best one of them all in my opinion). So to any of the ancient whovians if you have an answer please tell me.
After the new Progenitor Daleks escaped, they travelled to Skaro and rebuilt the Dalek Emperor, their city of Kaalann and later their whole Empire. The Eleventh Doctor discovered that the New Dalek Empire had invaded Earth in 1963. He went to the rebuilt city of Kaalann and discovered that the Daleks had found the Eye of Time, a Time Lord device that helped them alter Earth's timeline. Using the Eye, the Doctor was able to travel to Kaalann when it was ruined and before the Daleks arrived. He managed to sabotage the Daleks' vision, allowing him to deactivate the Eye. The timeline returned to normal and the New Dalek Empire and their invasion of Earth was erased. Skaro was also reverted to a ruined state, as it was before the Daleks arrived.
So we can assume that the time lock around Skaro was/is broken due to these events.