To really put this to rest:

Harakiri and Seppuku both literally mean abdomen/stomach cutting. Those who know some Japanese may recognize hara from the common phrase hara hetta which means you are hungry (literally, your stomach is decreasing in size or diminishing). Kiri means cut.

腹: hara 切: kiri

Seppuku simply reverses those kanji: 切腹

Why are they pronounced differently? Harakiri is a native Japanese word, using more traditional Japanese pronunciation Seppuku is a borrowing of middle Chinese roots: setsu from Middle Chinese tset meaning to cut, and fuku from Middle Chinese pjuwk, related to modern Mandarin fūk.

So, setsufuku was shortened to seppuku where the Ps represent a glottal stop and skipping of part of the word.