The main sticking point has been the Minister of Health's insistence that, if a player tests positive for the coronavirus, the entire team would have to go into quarantine for 14 days.
The Serie A clubs and the players' association says that this is not practical as it would take only a handful of positive tests in different teams to cause a flurry of postponed games.
They argue that, in countries where the re-start of the league has been authorised, only the infected player needs to be isolated.
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The clubs also want the government to drop a requirement that teams and their staff spend 15 days isolated in a training retreat before the league re-starts.
Serie A said that Friday's meeting took place in "an atmosphere of active collaboration."
"The points of the protocol that are difficult to implement were analysed and some tweaks were constructively elaborated in order to solve problems," it said in a statement.
It said the meeting had ended with an a proposal for alterations to the protocol which would be submitted to the sports and health ministries.
The protocol was initially drawn up by the FIGC but was described as insufficient by Sports Minister Vincenzo Spadafora and adjusted by the government.
Giorgio Chiellini et Mario Balotelli lors de Juventus-Brescia, le 16 février 2020
Image credit: Getty Images
"We had said many times that certain protocols were not feasible and we are pleased to see that the Serie A is behind us," said former Italy national team doctor Enrico Castellacci, the president of the Italian Football Doctors Association.
"What worries us, and we have represented this to Sports Minister Vincenzo Spadafora who has been receptive and considerate, is the issue of mandatory quarantine for the whole team in case of a new positive (test)," FIGC president Gabriele Gravina told state broadcaster Rai.
With 12 rounds of matches still to play, Gravina said that he could not rule out the season having to be settled with a playoff system instead of playing out the scheduled fixtures list.
"We must be ready for any eventuality," he said. "We'll have to weigh up the possibility of using a different way to finish the championship."