Santana has one week, until 4 p.m. CT on Nov. 11, to accept or decline the offer. It's expected that Santana will decline and test the free-agent market for a long-term contract.
The Royals have expressed strong interest in bringing back Santana, who had a 9-10 record but a 3.24 ERA and 23 quality starts among his 32.
"The process will unfold and we expect a decision to be made deeper into the free-agent season," Moore said.
Clubs can begin signing free agents, including Santana and Chen, as of 11:01 p.m. CT on Monday.
A qualifying offer means that if another team signs Santana, that team forfeits a top pick of the First-Year Player Draft -- a first-round choice for teams not selecting in the top 10, a second-round pick for those who are in the top 10. The Royals would not get that choice but would add a selection in the compensatory round between the first and second rounds.
In short, the qualifying offer and the pending loss of a Draft pick might make another team shy away from signing Santana.
Santana made $13 million last season. Chen's salary was $4.5 million.
While Moore has repeatedly said the team prefers to add players from within the organization or through trade, the Royals will scan the free-agent market.
They'll likely be looking to add a bat in right field, where such intriguing free-agent names as Carlos Beltran and Marlon Byrd might pique their interest and at second base, where Robinson Cano would be far out of reach but Omar Infante might fit.
If Santana and Chen depart, they'll feel added urgency to add starting pitchers as well.
The Royals also announced that pitcher Felipe Paulino was reinstated from the disabled list after undergoing surgery for removal of a cyst from his right shoulder in September. That ended his season after seven rehabilitation starts in the Minor Leagues as he returned from Tommy John surgery in July 2012.
Dick Kaegel is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.