The attacks in the Belgian capital on Tuesday are unlikely to have a long-term impact on markets, but they could result in new roadblocks to cross-border commerce and lend momentum to Euro sceptics, analysts told CNBC.

European stocks were under pressure but had come off their lows following deadly attacks at Brussels main airport and on the city's metro system. U.S. equities were mixed by late morning.

The attacks came four days after the arrest of Salah Abdeslam, a key suspect in the November Paris terror attacks.

European Union member states should close their borders until the continent gets the security situation under control, retired U.S. Army Col. Jack Jacobs said Tuesday.

"Once you are in Europe, the first place you land in Europe, you're wherever you want to go in Europe," he told CNBC's "Squawk Box." "It's been astonishing for decades, how the Europeans could be as complacent as they have been about security when the borders are completely and totally open."

More than 400 million EU citizens, as well as non-EU nationals, business travelers, and tourists, are able to travel throughout 26 European countries — known as the Schengen area — without having their passport or visa checked.

Maintaining security and holding the European Union together is a huge challenge with significant implications for U.S. multinationals, said Joseph Quinlan, chief market strategist for U.S. Trust of America Private Wealth Management.

"The European Union, the economy is $18 trillion. If it does become more difficult to move goods, people, and so forth, that's a big issue for the markets," he told "Squawk Box."

Michael Tyler, chief investment officer at Eastern Bank Wealth Management, said the attacks may feed fears in Britain about the perceived failure of European countries to integrate immigrants. At the time he spoke, no suspect had been identified.

Britain will hold a referendum on whether to stay in the European Union on June 23.

"I think it gives the exiters a little bit more momentum and a little bit more focus today," Tyler told "Squawk Box."

The market reaction will likely come only after there is a political response to the attacks, said Jason Trennert, Strategas Research chief investment strategist.

"I think globally there is clearly a re-evaluation of immigration policies," he told "Squawk Box." "This is a global phenomenon."

"There's no question that nationalistic tendencies and populist tendencies are going to get stronger," he said, adding that such a climate would make trade more difficult.

Boris Schlossberg, managing director at BKForex, said he, too, thought the fallout from the Brussels attacks may be more political than economic, though the long-term ramifications could ultimately rock Europe's economy.

If terrorist events yield nativist sentiment in Europe, it could feed the fervor to break up the EU, he said. A British exit would endanger the entire EU unification process, he added.

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