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Willis' time of 7:40.62 took more than four seconds off his previous best, a 7:44.90 indoors in Boston nine years ago. His best outdoor time stood at 7:45.97, set in Lausanne in 2005.
Willis placed tenth in the high quality field in the penultimate World Challenge meet of the European season. The race was won by Kenyan Caleb Ndikui in a meeting record of 7:35.06.
The time moves Willis up from fifth to second on the New Zealand all-time 3000m list, behind John Walker's New Zealand record of 7:37.49 set in 1982.
Willis found the extra distance tough.
"My body and mind were in shock once I passed the 1200m mark. The fitness is obviously there, but I hadn't done anything to prepare specifically for a race over a mile, so it felt like I was just hanging on for dear life," Willis said.
The Olympic silver medallist returns to the familiar distance of 1500m this weekend in the Italian city of Rieti.
"That [3000m] should hopefully bode well for my lone 1500m race remaining this season. Would be nice to knock the Commonwealth Games Qualifier out of the way a year in advance. Most guys are getting tired at the end of the season, but I seem to be just rounding into form."