He said New Zealand would have attended anyway, but he would use the visit to help push the council bid along. Sri Lanka being an important trading partner would not make him water down any criticism.
Amnesty International NZ's Grant Bayldon said it was not whether Mr Key would raise human rights with Mr Rajapaksha, but how loudly.
Mr Key's statements leading up to the event have been more subdued than those of his British counterpart, David Cameron, who has demanded Sri Lanka hold an independent inquiry into alleged war crimes.
Mr Bayldon said New Zealand needed to make a strong stand, especially given its sales pitch for the Security Council seat relied on its record as a strong, independent voice.
Before he meets Mr Rajapaksha, Mr Key will get a report back from Foreign Minister Murray McCully, who is travelling north today to meet Tamil leaders.
Mr McCully said the trip would give him a chance to assess whether progress towards reconciliation in Sri Lanka was genuine.
Mr Key said he would raise human rights issues with Mr Rajapaksha, questioning the sacking of the Chief Justice and what was being done to investigate any war crimes at the end of Sri Lanka's civil war.
If there was a challenge to Sri Lanka taking over as Commonwealth chair, he would assess it at the time before deciding what position to take.
Mr Key's wife, Bronagh, and son, Max, are flying with him to Sri Lanka.
Last night, Sri Lanka's media minister rebuked David Cameron, saying he could not make demands of Sri Lanka like a colony.
Keheliya Rambukwella told the BBC: "We are a sovereign nation. You think someone can just make a demand from Sri Lanka. It can be a cordial request. We are not a colony. We are an independent state."