The "siege-busting" shipment to blockaded Gaza was arranged by the Authority to Break the Siege, an alliance that includes all Palestinian political parties inside the Green Line - Israeli-Arab politicians and activists living within Israel.
Ahmed Tibi, an Israeli Arab MP, said: "We were preparing to set sail for the Gaza Strip to deliver hundreds of kilogrammes of medicines and basic goods and the maritime police stopped us weighing anchor.
"This is a cowardly act by people and the police who fear our delivery of medication to Gaza's Shifa hospital. But we will continue to try to break the siege."
Other Israeli Arab MPs, including Taleb al-Sana and Mohammed Barakah, were also on board the ship along with Jewish left-wingers and peace activists.
Micky Rosenfeld, an Israeli police spokesman, confirmed that the boat had been stopped and ordered to move to Tel Aviv marina where it was put under watch.
"We warned the boat's owner that he would be breaking the law and would be arrested if his boat were to try to sail to Gaza," he said.
Rosenfeld also said: "Three Israelis from the Galilee who had brought a lorry-load of food and medicine to the dock were detained for questioning."
"Checkpoints were set up and guards deployed at the other side of the port, preventing even reporters from entering"
Elias Karram, Al Jazeera's correspondent in Jaffa
Our correspondent said: "Israeli police forces, special forces patrols and anti-riot police are heavily deployed in Yafa's [Jaffa's] streets and ports.
"Sand barricades have been placed at one of the entrances of the port, an unusual activity at this small port. Checkpoints were set up and guards deployed at the other side of the port, preventing even reporters from entering it."
Prominent Israeli-Arabs and Knesset Arab MPs told Al Jazeera that they were heading to the port city in an attempt to persuade the authorities to let the ship enter Jaffa, load up and set sail for Gaza.
However, Karram said is seemed unlikely that Israel would allow the shipment to take place and that the Israeli-Arab coalition's aim in commissioning the ship was largely political.
Israel closed the border crossings with Gaza on November 4 following rocket attacks launched by Palestinian fighters within the Strip and has refused to lift the blockade until the attacks end.
Both sides blame each other for breaching a five-month old truce with Palestinians saying the increase in rocket fire was triggered by a deadly Israeli army raid on the territory.
Since the blockade was stepped up, Gazans have suffered routine electricity blackouts, food shortages and bank closures as fuel, food and cash reserves run out.