New Zealand won an entertaining game by five wickets inside three days but Muralitharan's run-out after he had left his crease to congratulate Kumar Sangakkara on his century was still the big talking point on the eve of the final Test in Wellington.
"From the team point of view it was black and white, it was a cricketing decision made on the field," New Zealand captain Stephen Fleming told the New Zealand Press Association on Thursday.
"It's a mistake by them and they covered it up by taking the moral high ground."
Fleming said Sangakkara had batted selfishly to create the situation.
"It was a 'selfish' act that got Sri Lanka in that situation in the first place," Fleming said.
"Sangakkara was batting so well and so easily and then he decides to take a single off the first ball to create an opportunity which maybe puts the player ahead of team. The guys were interested in his comments to deflect that.
"We won a good Test match down there and it's been diluted by that situation. We're very proud of any Test win we get and to have that not mentioned or talked about is annoying."
Sri Lanka captain Mahela Jayawardene maintained his view that the runout was against the spirit of cricket. I've played enough cricket to know that was unsportsmanlike," he said.
"The ball was live, but there are various other ways of getting batsmen out."
"It's over for us now. If Stephen wants to talk about it then he obviously has something in his mind which is bothering him."
Fleming believes the incident will make his team more determined to complete a 2-0 series whitewash.
"The fact it's been talked about adds a little bit of steel to our determination," he said.
"We'll look to be as intense and aggressive as we can. We weren't convincing winners, there's still enough areas of concern to have us twitchy going into this game."
Fleming said subject to a final inspection he would be keen to bowl first in Wellington, which would almost make the toss redundant as Jayawardene wants to bat first regardless of conditions.
The Sri Lankan skipper's philosophy is to give his proven match-winner Muralitharan last use of a wearing pitch - a policy which backfired in Christchurch where the New Zealand seamers ensured the Test was over inside three days.
The teams play two Twenty20 internationals before a five-match one-day series starting on Dec 28 in Napier.
New Zealand: Stephen Fleming (capt), Craig Cumming, Jamie How, Mathew Sinclair, Nathan Astle, Jacob Oram, Brendon McCullum (wk), Daniel Vettori, James Franklin, Shane Bond, Chris Martin and Iain O'Brien.
Sri Lanka: Mahela Jayawardene (capt), Sanath Jayasuriya, Upul Tharanga, Kumar Sangakkara, Tillekaratane Dilshan, Chamara Kapugedera, Chamara Silva, Prasanna Jayawardene (wk), Farveez Maharoof, Chaminda Vaas, Lasith Malinga, Dilhara Fernando, Akalanka Ganegama and Muttiah Muralitharan.