Leaving behind a storm of controversy over flying the Palestinian flag in his city hall, the mayor of Dundee, Scotland, crossed into the West Bank from Jordan today carrying a bottle of Scotch, a municipal chain given by King George V and stiff determination to officially twin his city with Nablus, the largest Arab town in the West Bank.

"Welcome to Palestine," greeted Nablus Mayor Bassam Shaka, after Dundee's lord provost, James Gowans, crossed the Allenby Bridge for a four-day visit here and in the West Bank.

Dundee, the fourth-largest city in Scotland, has been in an uproar since the city council approved a town-twinning arrangement with Nablus, a center of Palestinian nationalism in the occupied West Bank, and hung the Palestinian flag alongside those of the United States, France, West Germany and Yugoslavia.

Nobody objected when Dundee started twinning in the 1960s, first with Orleans, France, and then with Wuerzburg, West Germany. And everybody seemed to agree with the plans to twin with Highland Park, Mich., although some eyebrows went up when Zadar, Yugoslavia, became the third twin.

But when Nablus entered the fold, "all hell broke loose," according to George Galloway, secretary of Dundee's Labor Party.

The leadership of the Dundee Jewish community charged that the Nablus twinning has encouraged an outbreak of anti-Semitic vandalism and swastika painting in the city of 196,000 and has protested to British Home Secretary William Whitelaw.

The twinning also attracted attention in Israel, where the Palestinian flag is considered provocative and a symbol of the Palestine Liberation Organization's resolve to dismantle the Jewish state. The flag is banned by the military government of the West Bank and is rarely seen there.

Gowans and four other Dundee officials were greeted at the Allenby Bridge by Shaka, who lost both legs in a June 2 car bomb explosion, and by Ramallah Mayor Karim Khalaf, who lost a foot in a simultaneous blast. Both assassination attempts are believed by Israeli authorities to have been the work of untranationalist Jewish settlers.

At a luncheon today, there were frequent reminders by the Arab hosts that Britain, which lost its mandatory authority over Palestine in 1948 with the creation of Israel, played a major role in the birth of the current impasse between Arabs and Jews.

Referring to Israeli Prime Minister Menachem Begin, Khalaf declared, "He is a terrorist who came here from Poland in 1943 and killed British soldiers."

Apparently unmindful that Shaka abides by Moslem strictures against alcoholic beverages, Gowans presented the Nablus mayor with a bottle of Scotch. The Dundee mayor denied there was any anti-Semitism in Scotland and said vandalism of the sort reported by Dundee synagogues has hit all parts of the city. He said Nablus was picked as a twin because Shaka met with city officials and gave them a flag when he was hospitalized in England.