Arab leaders said the clash had been triggered by undercover police who began thowing stones from among the demonstrators -- a tactic that the unit has been caught on film using at protests in the West Bank.
Mohammed Zeidan, head of the Higher Follow-Up Committee, the main political body for Israel's Arab citizens, who comprise a fifth of the total population, condemned the police actions.
"Racism is no longer found only in documents or on the margins, like with Marzel, but has become a phenomenon among decision-makers and carried out on the ground. What happened today in Umm al-Fahm is a menacing escalation."
Police said nine Arab demonstrators had been arrested for stone-throwing.
Four police officers were reported to be lightly injured. The far-right marchers were escorted away by police, unharmed.
Ms Zoubi, a first-term MP, shot to notoriety this summer after she was among the first passengers to be released following Israel's violent takeover of the Mavi Marmara.
Ms Zoubi contradicted the Israeli account that the nine passengers had been killed by commandos defending themselves, accusing the navy of opening fire on the ship before any commandos had boarded. She also claimed several passengers had been allowed to bleed to death.
She was provided with a body guard for several weeks after receiving a spate of deaths threats and general villification in the parliament.
The Israeli police have been criticised in the past for lying about the strong-arm methods used to quell protests by the country's Arab citizens.
A state commission of inquiry found in 2003 that the police had used live ammunition and rubber bullets, in violation of its own regulations, to suppress solidarity demonstrations inside Israel at the start of the second intifada.
Thirteen Arab citizens were killed and hundreds injured in a few days of clashes in 2000. Police had falsely claimed that the deaths had been caused by "friendly fire" from among the demonstrators.
A recently parliamentary report revealed that there were only 382 Muslims in Israel's 21,000-strong national police force or less than 2 per cent.
The establishment of the undercover "mistarvim" unit against the country's Arab population caused outrage among civil rights groups when it was first revealed last year.
The far-right march in Umm al-Fahm was timed to coincide with the twentieth anniversary this week of the assassination of Rabbi Meir Kahane, who founded Kach. At a commemoration service in Jerusalem on Tuesday, Rabbi Yisrael Ariel told hundreds who attended that the government was allowing the Palestinians to "establish an Ishmael state in Israel".
A version of this article originally appeared in The National (http://www.thenational.ae), published in Abu Dhabi.
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