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Kitahara (Neptune) won the men's 13-14 years 50m backstroke, 100m and 200m breaststroke, 200m individual medley and 100m backstroke, while Govaerts (Zenith) had similar success in the men's 15-16 years bracket.
He won the 50m backstroke, 100m breaststroke, 200m freestyle, 200m individual medley and 50m freestyle.
The 15-year-old had to share the spoils in the 50m freestyle with Noel Bisson (16) of Wanaka, as the pair touched the wall at the same time in 26.38sec in a thrilling finish.
Matthew Glassford (24), of Neptune, also had plenty of success through the first three days, winning the men's 17 years and over 50m backstroke, 400m freestyle, and the 100m and 200m breaststroke.
The two provinces are holding their championships together for the fourth straight year since the February 22, 2011 Christchurch earthquake destroyed the QEII pool, leaving the city without a 50m long-course pool.
In each of the five morning sessions, swimmers from all three provinces compete in timed finals together, but their results are segregated.
Olivia Gold (16), of Neptune, showed good speed over 50m to win the women's 15-16 years 50m freestyle, pipping Devon Familton (15), of Neptune, and Sophie Fairbairn (15) of Wanaka, in the process.
Later, Fairbairn got the better of Familton and Gold in the 50m breaststroke, winning in 36sec.
Despite missing out in the 50m freestyle and 50 breaststroke, Familton has won an impressive five races in the women's 15-16 years category. She won the 200m individual medley, 50m and 100m backstroke, 200m breaststroke and the 100m butterfly.
Isobel Ryan (18) of Oamaru, and Kate Godfrey (21) of Neptune, have had some good battles in the women's 17 and over age-group.
Ryan got the better of the Neptune swimmer in the 50m freestyle and 50m backstroke, before Godfrey turned the table in the 100m backstroke and 200m freestyle.
Cecilia Crooks (14) of Neptune, and Caitlin Deans (15) of Neptune, have also been impressive.
Crooks won the women's 13-14 years 200m individual medley, 50m freestyle and 100m backstroke, while Deans won the 400m freestyle, 50m and 100m backstroke and 200m freestyle in the women's 15-16 years category.
Among other Otago swimmers to impress over the first three days were Mila Jojic (13) of Queenstown, Cameron Jones (20) of Neptune, Ella Rose Lawrence (13) of Clutha, Saskia Turner (17), of Neptune, Tandia Gooch (14) of Oamaru, Cameron Moran (14) of Neptune, Samuel Wardhaugh (15) of Neptune, Jeremy Tasker (20) of Neptune, Gabrielle Trotter (14) of Neptune, Nick Pryde (15) of Neptune, Danielle Walsh (14) of Neptune, Madeline McCane (13), of Kiwi, Ben Carr (15) of Neptune, Erin Ford (15) of Kiwi, and Matt Robinson (15) of Clutha.
The championships finish tomorrow afternoon.