The Argentine admits he would have preferred Sandro Rosell to remain as president but has stressed the team will be inspired to perform better this weekend
The Spanish champions were rocked by the resignation of president Sandro Rosell this week as the investigation into Neymar's transfer to the club continues.
Martino admits he would have preferred Rosell to remain in his post and conceded he could make no assurances over his own long-term future at Camp Nou.
"Everyone wants to finish a project they start, but in the world of football you cannot guarantee anything," the Argentine told a press conference.
"It's not an ideal situation. Everyone wants to do a good job and finish together. I respect the president's decision.
"I spoke with him before he announced his resignation. He always showed great confidence in me. I would have preferred it had we stayed together, but it could not be so. He told me he resigned for the same reason he told you journalists.
"Rosell showed me his support, but I say the same for Andoni Zubizarreta and the new president, the people with whom I've spoken with most since June."
Martino revealed the squad have been hurt by the fallout from one of the more turbulent weeks in Barcelona's modern history but stressed they would be motivated to perform even better in order to put the controversy behind them.
"The players are saddened by the situation, but they know the best way forward is to do things right from a footballing point of view," he added.
"I know where I'm coming from and what I focus on is making the team do well. The match against Malaga is more important than the president. Perhaps it will make the team stronger."
Martino also claimed that Neymar, who is currently sidelined with an ankle injury, would not be affected by the ongoing investigation once he returns to first-team action.
"We must emphasise the attitude of Neymar and his father to give their permission to reveal the numbers [of the transfer], but I don't believe it will affect his performance," he added.