Marshallese government and American Army security guards late Sunday evening arrested 13 of some 400 landowners and their families who had begun a sit-in at their properties on Kwajalein Island, headquarters of the U.S. Pacific Test Range.

Despite the arrests, similar sit-ins, involving about 100 additional Marshallese, were reported yesterday to have spread to three other islands in Kwajalein atoll, whose wide lagoon is the target for warheads of strategic missile tests launched from Vandenberg Air Force Base, Calif., some 4,200 miles away.

The sit-ins have caused President Amata Kabua and key cabinet members to fly to Kwajalein to attempt to resolve the situation before it has an impact on the American missile test program.

The demonstrators are unhappy with the financial settlement reached last month between negotiators for the Marshall Islands government and the United States that provided for continued use of their land on Kwajalein.

The Kwajalein landowners had an interim agreement for the last three years to rent their land to the Marshalls government which in turn made it available for American use. Under that arrangement, which ran out last September, the landowners received $9 million per year.

As part of a broader arrangement between the Marshalls and the United States, Kabua's negotiators last month agreed on behalf of the Kwajalein landowners to continue for 30 years the annual rent of $9 million.

The landowners, who wanted the rent raised to $16 million, have announced they would oppose the Kabua agreement and Ataji Balos, chairman of the board of the Kwajalein Atoll Corp., resigned as minister of internal security of the Marshallese government so he could lead opposition to the pact.

Balos was one of those arrested Sunday evening. His wife wired President Reagan yesterday from her Honolulu home asking him to "suspend" the testing of a Minuteman II missile which she said was supposed to take place today.

A Pentagon spokesman said yesterday that he could not "discuss in advance" any test shots. But another official confirmed that a warning had been given to ships in the area to avoid Kwajalein for the next few days, a sign that some testing activity is expected.

Balos's wife told the president that she wished that "all nuclear weapons testing at Kwajalein would stop forever."

Three years ago, islanders conducted a six-week sit-in after which the annual rent paid to Kwajalein landowners skyrocketed from $740,000 a year to the current $9 million. During those six weeks, however, the U.S. missile testing program was suspended.

Although there have been attempts in the past to enroll the Marshallese in antinuclear weapons protests that would bring a permanent end to missile testing at Kwajalein, the multibillion-dollar American facilities spread through the atoll's many islands provide a major source of jobs and income to the Marshall Islands.