National Bank originally bought the portrait in the 1970s and was put into the ANZ archive when the banks merged, MOTAT library and archive manager Simon Wetherill told Morning Report.
"As it happens a lot of the time, it sometimes can be forgotten about."
Upon discovery it needed to be reframed and had "a bit of a clean up" but was in remarkably good condition, he said.
The painting portrays Batten just on the cusp of her significant South Atlantic flight in November 1935 and after her flight from England to Australia in 1934.
"This is her at 36 years old looking confident, looking pretty strident really, about to embark on the next two big flights that really made her name."
It's not obvious that Batten is an aviator in the painting, something that Wetherill says makes it unique.
"There's nothing that indicates anything to do with aviation in the background, even in the clothing that she's wearing. It really is quite a striking portrait of this confident young women."
Where the painting was held before it came into the hands of National Bank, Wetherill said is a mystery.
The portrait is on display at the Walsh Memorial Library at MOTAT.
