The two never met with Clune, 34, and responded saying they felt uncomfortable, Harkins said. They also told school authorities, who notified police Monday, authorities said.
On Wednesday, police arrested Clune at his Gloucester Township home and charged him with harassment for inappropriate conduct with a juvenile. Police announced the charges Friday.
The 18-year-old did not press charges but could do so within a year, Harkins said.
Clune had not contacted either female with text messages or on Facebook during the school year, police said. Harkins said there was nothing "blatantly sexual in nature" about the messages. "They were flirtatious," he said.
Clune sent 33 text messages to the juvenile from July 4 through Monday, and sent 39 private Facebook messages to the 18-year-old from July 4 through last Saturday, police said.
Harkins said most of the messages were short ones on July 4. The messages resumed after a break of a day or two, Harkins said, before the two graduates ended the conversations.
A letter Friday from the Black Horse Pike Regional School District, which has three high schools, alerted the community and said Clune had been suspended.
Clune, also Timber Creek's boys' baseball coach, was directed not to have any further contact with students and staff and to stay off school grounds, superintendent Brian Repici wrote.
"We take an aggressive stance against any employee who makes inappropriate contact with a student," Repici wrote.
Clune was processed and released on a criminal summons. The disorderly persons charge carries fines and up to six months in jail.
No one answered the door Friday at the Clune home on Chestertown Road. A call to the home was not returned. Clune is married.
Clune's father, William, described his son as "an excellent person and a good teacher."
Clune's Facebook page said he graduated in 2003 from Rutgers-Camden. He has been at Timber Creek since then.
Natalie Dougherty, who lives a few doors from Clune, said he was always neighborly. "He always said, if the kids needed extra help with math, give him a call," said Dougherty, a registered nurse.
Donna Spencer, a special-education teacher who lives next door to Clune, said she was upset and hoped the allegations were not true. Clune taught her son six years ago, she said.
"You're supposed to educate and mentor students and help guide them," she said.
It is the second time in 15 months that a district teacher has been charged with inappropriate behavior.
In April 2012, three teachers at Triton Regional High School and two administrators were charged in a sex scandal. The male teachers were engaging in sexual acts with female students, police said. The principal was charged with failing to report the crime. A former vice principal was charged with official misconduct, but charges were dropped in exchange for her resignation, authorities said.
Gloucester Township police asked anyone who might be a victim of inappropriate conduct with Clune to call 856-228-4500.
Contact Darran Simon at 856-779-3829 or firstname.lastname@example.org, or follow on Twitter @darransimon.