"The foreign ministry has sent a written protest to the Syrian embassy in Amman after a shell landed Thursday night on Al-Falah mosque, near the industrial park in the northern city of Ramtha," Mohammad Momani said in a statement carried by state-run Petra news agency.
"The shell hit that area during clashes between the Syrian troops and the (rebel) Free Syrian Army."
In what Petra termed its "strong protest," Momani said the foreign ministry "stressed the need to take measures to prevent such incidents in the future."
In August last year, four rockets fired from Syria crashed inside a Jordanian northern border area, wounding a young girl and sparking an earlier letter of protest.
Jordan is home to more than 500,000 Syrian refugees.