Sandro Rosell resigned as the club's president in January as he faces legal action for misappropriation of funds, whilst Barca were also charged with tax fraud over the deal.
The Brazilian was also sidelined by an ankle injury for a month at the start of the year and Martino also thinks that has also played a part in the 22-year-old's return of just one goal in 2014.
"Returning after a month out injured it is always difficult to get back into rhythm and then the problems with his signing appeared," he said at a press conference on Saturday.
"If I had to choose one reason I would focus in the non-sporting issues."
Neymar was only one of a number of Barca players who were well below par as the Catalans lost 1-0 to Valladolid last weekend.
That defeat left them four points adrift of Real Madrid at the top of the table and Martino admitted they must beat Osasuna at home on Sunday to remain in the title fight before travelling to face Real next weekend.
"Osasuna is a final for us to be able to get to the Madrid game with a chance.
"They have caused problems to everyone, especially against the top three at home. We expect a difficult game and we will have to work hard."
Gerard Pique has been left out of Martino's 18-man squad due to a slight ankle injury, but the Argentine insisted it is just a minor problem and the Spanish international should be fit for next weekend.