He was the fastest in the bunch sprint, which decided stage 13 from Rincon de Soto to Burgos, ahead of Norway's Thor Hushovd and Italy's Daniele Bennati.
But Cavendish, leading in the points competition, complained that American Tyler Farrar of the Garmin-Transitions squad and Belgian Wouter Weylandt of the Quick Step team had joined forces against him.
"Wouter's helping Farrar and that's going to make it more difficult for us to control the points competition," Cavendish told Reuters.
"If you've got two guys from different teams working together that's always going to be harder."
Cavendish made an official protest to race officials about an intermediate sprint early in stage 13, at Calahorra, when he said the two blocked him in but said it was unsuccessful.
"One went left, the other went right and they deliberately closed the door on me."
"I've never ever made a protest about this sort of sprint before but I feel I was put at a disadvantage."
Garmin-Transitions and Quick Step were not immediately available to comment.
Cavendish's overall lead in the points competition is now 21 ahead of Farrar.
"It's a nice cushion but I'll take every stage as it comes." he told reporters.
Spain's Igor Anton retained the overall race lead ahead of Italian Vincenzo Nibali and Spaniard Xabier Tondo.
"Anton could get points in the upcoming mountain stages although there's still a couple more sprints to come," added Cavendish.
"But, unfortunately, now Weylandt's actually working for Farrar in the intermediate sprints that's a disadvantage."
Cavendish did not let his disappointment over his rivals alleged tactics stop him from 'bunnyhopping' over the finish line as he secured his 10th win of the 2010 season.
"I just like to do special victory salutes like that," he told reporters.
"I did one in the Tour de France for (team co-sponsor) HTC last year, and it's nice to be able to give something back to people who do something for the sport."
The 25-year-old also praised team mate Matt Goss of Australia who, for a second successive day, guided Cavendish through the pack to a winning position.
"We'd done our homework and we knew that last corner was wide. Everybody braked but Goss went straight up the inside at a phenomenal pace."
"It was hard for me to stay on his wheel at one point and I had to sprint a little bit later because I was a little bit in the red."
"But he did an incredible job, as did the other guys, and we could get the win."
The Tour of Spain finishes on Sept. 19 in Madrid.
