Benitez's side - the league leaders on goals scored after two wins - are preparing to host the ninth-placed Atalanta, and should have the services of Hamsik, who was on international duty in mid-week.
Hamsik scored in Slovakia's 2-1 World Cup qualifying loss to Bosnia-Herzegovina in Zilina on Tuesday after playing against the same country in Zenica on Friday, but Benitez said the 26-year-old had returned to the Stadio San Paolo in good condition.
"When the players get back after the matches with their national teams, they usually complete a less intense training session," the former Liverpool and Chelsea coach said.
"Hamsik has made a standard training session with the other guys who have got back yesterday.
"By saying standard, I mean that he has worked as usual, only less intensely compared to the other guys who were here from the beginning of the week.
"Today we'll have the second training and we'll see the condition of everyone and see if someone has any problem.
"As of yesterday, all players were in good conditions, including Hamsik."
Benitez said he was not bothered by what system Atalanta would play, declaring them defensively sound but also capable of damage up front, with the likes of Giacomo Bonaventura, German Denis and Marko Livaja headlining their attack.
"There is no problem for me if they play with one module or the other, but of course Atalanta is a strong team with a wealth of experience, especially in the defence department," he said.
"As far as the forward department is concerned, they have three strong forward players and can always score goals."
Benitez said his players should be keen to perform early on in the campaign in order to sew up a starting XI spot for the remainder.
"All players should be focused on making a good performance in this match because it means that they would have more chances to play more matches," he said.
"If they don't have the right behaviour in this match, they will give me a bad message.
"But I believe that they know that in order to play about 44 matches from now till the end of the season, they should be focused on making a good job in every match."
