Melandri, who joined Ducati from Gresini Honda this year, is having difficulty acclimatising to the GP8 and qualified slowest of all at Jerez this weekend, having also crashed during the session.
But Suppo is adamant that it is just a matter of time before Ducati and Melandri make a breakthrough.
"I cannot believe that we will not solve the situation," he told autosport.com.
"Marco has the talent and Ducati has the capability to adapt the bike more to his style, so I cannot believe that the situation will not change."
Suppo said the fact that Melandri was behind the satellite Alice D'Antin Ducatis of Toni Elias and Sylvain Guintoli emphasised how much he was struggling.
"It's difficult to understand why, but with all respect to Guintoli, Marco should be at least one second faster than Sylvain," he said. "If he was one second faster it would be a more reasonable situation."
The team boss fears that the longer Melandri's difficulties go on, the harder it will be for the Italian to get on the pace.
"The more you win, the stronger you become. The more you struggle, the more difficult it becomes to solve it," Suppo said.
"For sure it doesn't help that we start the season with two circuits where the package is not 100 percent, especially here."
autosport.com
