Shepparton's total June rainfall was 39.6 mm, slightly higher than the June average of 37.7 mm.
Benalla was also above its average of 50.8 mm, receiving 55 mm, however, Echuca had 29.1 mm, below its June average of 42.4 mm.
Rainfall levels last month were below average in large parts of Victoria; 26 per cent below the long-term June mean of 59.4 mm.
Despite the lower levels of rain in June, the year-to-date rainfall total is about 350 mm — 22 per cent above average.
Hunters Hill in north-east Victoria recorded the highest daily rainfall total for the month — 62.2 mm on June 21.
June was characterised by warmer than average days and cooler than average nights.
Many parts of Victoria experienced large areas of frost on June 9, when night-time temperatures plummeted due to clear skies and light winds under a strong high-pressure system.
Bureau of Meteorology long-range forecasting manager Andrew Watkins said there was a 50 per cent chance of La Niña forming in 2020 — double the normal likelihood.
“Tropical Pacific Ocean surface temperatures have cooled in recent weeks, and models suggest this cooling will continue through winter and into spring,” Mr Watkins said.
A La Niña event typically brings above average winter-to-spring rainfall for Australia.
The 2010 to 2012 La Niña event saw Australia's wettest two-year period, with widespread flooding in many parts.
July is expected to be drier than average but August is forecast to be a wetter month.