Kerr was charged with causing a police officer harassment, alarm or distress during an incident in south-west London on January 30th last year, according to the Crown Prosecution Service.
Kerr denied the charge at a plea and trial preparation hearing at Kingston upon Thames Crown Court on Monday.
"Sam has our full support. She knows that. It's a difficult time for her," Hayes said on Wednesday.
"Of course, I can't comment, you know that. I can say I know she's pleaded not guilty and I don't want to do anything to jeopardise anything for Sam by speaking about it.
"For that reason, I'm sure you can appreciate that's all I'm going to say on the matter, but she has our full support, she knows that, it's really important I get that across. It's something I really value."
The alleged incident occurred before last year's World Cup, which was held in Australia and New Zealand, but was not publicly disclosed until now.
A Metropolitan Police spokesperson said the incident involved an officer who was responding to a complaint about a taxi fare. Kerr is expected to face trial in February 2025.
Football Australia CEO James Johnson called the allegation "unsettling" and "very serious".
"There's difficult moments, tough times, and that's what my role is at this football club, to make sure I look after our people, and I want to make it clear that Sam will be supported by me and everybody else," Hayes said.
Kerr is currently recovering from an anterior cruciate ligament injury suffered in January during Chelsea's training camp in Morocco.
The 30-year-old, born to an Anglo-Indian father and Australian mother, is a popular figure in Australia and one of the most famous players in women's football.
