Political unrest in the Middle East and Japan’s natural and nuclear disasters have raised questions about how exchange traded funds (ETFs) operated through these crises.

The complex drama in Van Eck’s Market Vectors Egypt Index ETF (NYSEArca: EGPT) while Egypt’s stock market was closed for seven weeks provided a solid test.

The fund continued trading while Egypt’s market was shuttered and the portfolio managers used so-called fair-value pricing to determine net asset value (NAV).

The NAV for the Egypt ETF “changed throughout the long period of market shutdown, indicating that fair value pricing likely was being used — though ascertaining ‘proper’ prices for some Egyptian stocks that hadn’t traded in weeks couldn’t have been easy,” writes Morningstar’s Gregg Wolper in a Fund Spy column this week.

Edward Lopez, Van Eck’s marketing director, confirmed the company determined fair value for the portfolio while Egypt’s market was closed. ETFs disclose estimates of their NAV every 15 seconds during the trading day.

During an interview this week on the sidelines of IMN’s 2nd Annual World Series of ETFs & Indexing conference in Boston, Lopez explained Van Eck can look at factors such as the movement of the Egyptian pound, other markets and correlations as well as news and material events. Also, some of Market Vectors Egypt Index ETF’s holdings are listed in London and Canada.

Egypt closed its stock market in late January with the last trading taking place on Thursday, Jan. 27. The Egyptian market is typically closed on Friday and Saturday, but is open on Sundays.

Over the weekend, authorities said the market would not open Sunday, Jan. 30, amid protests calling for the ouster of Hosni Mubarak, Egypt’s president.

However, Van Eck had accepted investor cash on Friday, Jan. 28, and was unable to put that money to work.

On Monday, Jan. 31, Van Eck announced the Egypt ETF was halting the creation of new shares, although it would honor redemptions. Shares of the ETF continued to trade on the secondary market while Egypt’s stock market remained closed.

However, the temporary suspension of share creation resulted in the ETF trading similar to a closed-end fund. A premium of over 10% to NAV developed and at times reached the 20% range. [Egypt ETF Trades At Premium Over NAV.]

The premium to NAV reflected buyer demand for the ETF but also added an extra risk for traders not normally associated with ETFs.

Market Vectors Egypt Index ETF resumed creations last week as Egypt’s market finally reopened, despite a quick plunge that triggered exchange circuit breakers. [Egyptian Market Opens: What About The ETF?]

The premium to NAV was reduced as “the arbitrage mechanism kicked in,” Van Eck’s Lopez said as the reopening of the Egyptian stock market allowed ETF market makers to arbitrage away price discrepancies.

Still, the premium was 2.8% as of March 29, according to Van Eck’s website.

The ETF’s cash position is below 1% with Egypt’s market back open and Van Eck able to deploy the roughly 40% cash stake that had built up while the market was closed.

Assets in the Egypt ETF have risen to $57 million while trading volume has exceeded 1 million shares on three occasions so far in 2011. Before the crisis hit, the ETF rarely traded more than 100,000 shares.

Lopez at Van Eck said the ETF did what it was supposed to do while acting as a “price-discovery mechanism for Egypt” while the underlying market was closed.

“A crisis creates both opportunities and risks,” he said.

Market Vectors Egypt Index ETF was down 19.3% year to date as of Tuesday’s close, according to Morningstar.