By Doyinsola Oladipo and David Shepardson

(Reuters) -U.S. East Coast and Gulf Coast ports were reopened on Friday after dockworkers and port operators reached a wage deal to settle the industry's biggest work stoppage in nearly half a century, but clearing the cargo backlog will take time.

The strike ended sooner than investors had expected, weakening shipping stocks as freight rates were no longer expected to surge.

"The port strike ended fairly quickly, removing any significant downside risk to the economy this quarter," said Ryan Sweet, chief U.S. economist at Oxford Economics.

At least 54 container ships had lined up outside the ports as the strike prevented unloading, according to Everstream Analytics, threatening shortages of anything from bananas to auto parts. More ships are sure to arrive.

Pricing platform Xeneta said it was likely to take two to three weeks for the normal flow of goods to be reestablished.

"Remember that ships keep calling, so it's not just a matter of handling the ships already in line, but to work extra hard to run down the congestion before supply chains are rerunning," Xeneta Chief Analyst Peter Sand told Reuters.

The International Longshoremen's Association workers union and United States Maritime Alliance (USMX) port operators announced the deal late on Thursday. Sources said they had agreed a wage hike of around 62% over six years, raising average wages to about $63 an hour from $39 an hour.

The ILA launched the strike by 45,000 port workers, their first major work stoppage since 1977, on Tuesday, affecting 36 ports from Maine to Texas. JP Morgan analysts estimated the strike would cost the U.S. economy around $5 billion per day.

The disruption was a headache for Democratic President Joe Biden's administration ahead of the Nov. 5 presidential election pitting Democratic Vice President Kamala Harris against Republican former President Donald Trump. It threatened to dent U.S. employment figures in a report due to be released shortly before Election Day.

The White House had put pressure on the USMX employer group to sweeten its contract offer to end the strike, as business trade groups warned of devastating consequences if the stoppage continued.

Shares in shipping companies in Asia and Europe fell after the deal was announced.

Shipping group A.P. Moeller-Maersk for example fell 4.7% by Friday morning, while Hapag-Lloyd was down 14.4%. Japan's Nippon Yusen, which had hit a record high a day earlier, shed 9.4% and Kawasaki Kisen fell 9.7%.

"Shipping stocks had previously rallied on expectations of price increases triggered by the strike by U.S. dockworkers and the tense situation in the Middle East," said Taishin Securities Investment Advisory analyst Tony Huang.