Hodgson chose to rest five key players for the 2-0 defeat at the KC Stadium, which allowed Hull to pull level with Gianfranco Zola's relegation threatened side on 27 points.
Bobby Zamora, Danny Murphy, Damien Duff, Aaron Hughes and Dickson Etuhu all missed the defeat but returned for last night's 2-1 win over Wolfsburg, which prompted the West Ham United hierarchy to claim that Hodgson broke Premier League rules.
A Premier League spokesman said: "We can confirm that we have received an official complaint from West Ham over this matter.
"We will now ask Fulham for their observations and then the Premier League board will then consider what actions, if any, are appropriate."
Premier League rules state that all teams must field their strongest side available for all games.
Should they find Fulham guilty, the Premier League could decide to impose a penalty similar to the £25,000 suspended fine handed to Wolves after Mick McCarthy rested nine of his players for his side's defeat at Manchester United in September.
Hodgson insisted last night that he had done nothing wrong and was adamant that he would continue his rotation policy for this weekend's match against Wigan.
"Firstly I don't think West Ham should be picking our team and I think that is a fairly obvious statement," said the 62-year-old.
"If there is a complaint my conscience is perfectly clear on the subject and as far as I'm concerned we don't have a case to answer.
"In the last game I selected a team comprising of a defender just sold for £10m (Chris Smalling), a South African international (Kagisho Dikgacoi), who replaced Danny Murphy and I replaced Bobby Zamora with Clint Dempsey, a USA centre forward.
"I can't understand why, if you have a large squad, it's not allowed for you to change things around. I can't imagine anyone questioning Liverpool, Manchester United or Chelsea for using all the players in their squad."
Hodgson has also found support from his peers, with Wigan manager Roberto Martinez describing West Ham's move as "foolish".
The Spaniard said: "As a manager you always make decisions that can help your team.
"Roy Hodgson and Fulham have had such a successful season, they know exactly what they have got behind the scenes and know what they need.
"For anyone to criticise another football club when they are in such outstanding form is very foolish.
"Roy Hodgson has got to make the decisions to help his team achieve their aims for the season."
The argument is the latest in a series of squabbles between the two clubs. Fulham are suing West Ham for £500,000 - the loss of their league position bonus three seasons ago after Carlos Tevez's goals helped keep the Hammers up and finish a place above Fulham in the Premier League.
The Premier League fined West Ham £5.5 million for breaking their rules over third party agreements over the deals which brought Tevez and Javier Mascherano to Upton Park but chose not to dock the club any points.