ST. PAUL — The leader of Minnesota’s health insurance exchange said Wednesday that some portion of its customers won’t be able to nail down coverage ahead of a March 31 federal deadline by using its troubled website, and will need to do so by filing a paper application.

“First and foremost, we want people to use the online system,” Scott Leitz, the interim CEO of MNsure, told its board of directors. “But we want to be honest: There’s going to be folks who aren’t going to be able to.”

The MNsure website has been plagued by technical glitches that in recent weeks frustrated the efforts of thousands of Minnesota residents seeking to sign up for insurance under the new federal health care law.MNsure officials said Wednesday that most problems have now been resolved for people who wanted insurance starting Jan. 1 — the first day coverage was available under the new law — but he said they are expecting an even greater crush of activity ahead of the March 31 deadline. People who don’t have health insurance after that date face a federal tax penalty.

“What we saw at the end of December was a spike in the number of folks seeking coverage,” Leitz said. “We anticipate that again, but more extreme, starting in the month of March.”

The MNsure website has experienced a host of bugs and glitches in processing and completing applications, from problems transferring information to insurance companies, to erroneous calculations of tax credits and coverage eligibility, to questions about security of information entered on the site.