"It was a bit difficult to tell when we got there because of the contents of the building. We definitely think it was suspicious because there was no power to the building."
The fire had been referred to police to investigate.
Colourplus employee Melanie Nathan said the books would be a big loss for the Heart Foundation, who came every week to collect them.
"They got a big surprise this morning when they turned up. We get a huge amount every day so there would have been a lot [in the shed] - there would have been a week's worth of books."
Heart Foundation's Wairarapa heart health advocate Kit Cohr said books collected from the shed went towards the charity's annual book sale, with a small truckload usually collected each week.
"They are very generous letting us use their shed and their It's disappointing that books donated very generously have gone up in flames."
Masterton Detective Sue Mackle said not much was known about the fire at this stage but asked anyone who may have seen anything to contact police on 06 370 0378.