The Portuguese giants' coach says "notorious" methods are being used by officials to help out Primeira Liga competitors Benfica and Sporting Lisbon
The defending champions are currently three points off top spot at the halfway stage of the season, but their hopes of retaining the title were dealt a blow by a 2-0 defeat to Benfica last weekend.
That result gave their rivals a clear advantage at the top of the table, while Sporting are sandwiched between the leaders and Fonseca's side.
The head coach was far from happy with the outcome at the Estadio da Luz, with four Porto players booked and defender Danilo shown a red for two yellow-card offences - and, in an extraordinary outburst, Fonseca claimed that there is a conspiracy against his side.
"The treatment given to FC Porto is not the same as the other clubs," he told reporters ahead of this weekend's clash with Vitoria Setubal.
"It is notorious, and only those who do not want to see do not see it.
"There is a concerted effort to weaken Porto and help the other two clubs' [Benfica and Sporting's] campaigns."