Sharri Markson, a senior writer at The Australian, was detained for questioning by security officials at the Ziv Medical Centre in northern Israel on Thursday.
Markson was travelling with other Australian journalists on a week-long study tour organised by the NSW Jewish Board of Deputies and the Australia/Israel & Jewish Affairs Council.
Sources said Markson became "aggravated" during the "tense" incident in which security officials demanded she hand over her passport, mobile phone and notes.
"It was very intense and dramatic," a source said. "There was a major commotion and suddenly there was security everywhere."
Over 500 Syrians – including wounded fighters battling the Assad regime – have been treated at the Ziv Medical Centre in Safed, near the Syrian border.
In a briefing before the tour began, hospital staff told the journalists that the patients could be at risk upon their return to Syria if it became known they had sought treatment in Israel. The hospital uses elaborate methods to secretly transfer the patients in and out of Syria.
The eight journalists were instructed not to record the names of the patients or to take photos that could identify them.
Fairfax Media understands that during the visit, Markson broke away from the other journalists to speak to the patients without supervision and exchanged contact details with them.
This led to her being detained by security forces. Fairfax Media understands the incident was resolved following intervention by NSW Jewish Board of Deputies chief executive Vic Alhadeff.
Mr Alhadeff, who has returned to Australia, said: "Our paramount concern was for the safety and security of the Syrian patients.
"In that regard, we are very mindful of not disclosing their identity.
"There was an unfortunate misunderstanding but the situation was quickly resolved."
Australia/Israel & Jewish Affairs Council executive director Colin Rubenstein, who was not on the trip, confirmed a "kerfuffle" had occurred at the hospital.
He said the council representative on the trip told him Markson "took down the email address of a Syrian patient, security officials got wind of it and asked her about it on the way out".
"Most times it's very clear to all the participants what the guidelines are. It's never been an issue before.
"The condition of visiting the hospital is to respect and maintain the confidentiality of the patients' identities.
"If anyone's identity was disclosed it would put them at great risk – it's a brutal part of the world."
Other reporters on the trip included Daily Telegraph deputy editor Ben English, Fairfax Media federal politics editor Bevan Shields and Channel Seven reporter Alex Hart.
Markson, who was until recently The Australian's media editor, declined to comment.
She later tweeted: "The Syrian fighters took my details to keep in touch with a journalist when they return to Syria, where they're at war with Assad and Daesh.
"The Syrian fighters gave me theirs too. Israeli security were a bit heavy-handed, demanding I delete the details from my phone and notebook."
This is not the first time Markson, the daughter of celebrity agent Max Markson, has been involved in a controversial hospital visit. In 2005 she reportedly secured an interview with a victim of the London bombings by entering the hospital ward looking upset and carrying a bunch of flowers. The incident was later covered by the ABC's Media Watch program.
Markson also reportedly rifled through the bins of rival publication Cosmo when she was editing Cleo magazine.