Whitson, who was regarded as one of the top high school pitchers in the 2010 Draft, even said as much himself.
"I'm definitely ready to go, that's my plan," Whitson said in June. "Hopefully, they can get that done fairly quickly. It's all up to me then."
The Padres had said in recent weeks that they were hopeful that they would sign Whitson.
"All conversations indicated this would be a quick sign," Hoyer said.
Even as late as Sunday and likely later, Padres director of scouting Jaron Madison said he was optimistic a deal could get done.
In the end, the Padres were left without a top Draft pick.
Whitson will now, apparently, head to the University of Florida, where he had signed a letter of intent.
Oddly enough on Monday, the Padres did come to terms with sixth-round pick right-handed pitcher John Barbato, who had also signed a letter of intent to pitch at Florida. Barbato reportedly agreed to a deal worth $1.4 million.
Because the Padres didn't sign Whitson, they will receive a compensatory pick after the 10th overall pick in the 2011 First-Year Player Draft.
Major League teams had until 9 p.m. PT Monday to reach agreements with their Draft picks.
The Padres had originally slotted between $1.9 million and $2 million to sign Whitson, though Hoyer said on Monday the Friars' last offer to Whitson was more along the lines of what the eighth overall pick -- Houston's Delino DeShields -- got ($2.15 million), and, in all likelihood, probably higher.
"I don't know what changed," Hoyer said. "There is a sense of frustration. I'll be honest, we're really surprised. But I feel great about the way we handled this."
The Padres have reached an agreement with their third-round pick, right-handed pitcher Zach Cates from Northeast Texas CC. Cates has earned the largest bonus ($765,000) of any third-round pick from the First-Year Player Draft.
Cates is an intriguing pick, because he was primarily a catcher in high school and even in his first season at Northeast Texas CC. But he blossomed as a sophomore and landed on the Padres' radar.
"This was his first full year of just focusing on pitching," Madison said. "We actually had him evaluated higher than the third round. His delivery is really easy with no effort. He has a feel to throw strikes, and at times, his changeup is a plus-pitch."
Madison said Cates routinely sits about 92-93 mph with his velocity and will hit 97 mph on occasion.
As with Cates, the Padres went above the recommend slot when they signed their ninth-round pick, outfielder Jose Dore, last week for $450,000. Dore had committed to playing for Florida State.