"The only solution is to keep working hard. The problem is the timing. We should be fixing these issues in January, not in March."
McLaren, who have won a combined 20 drivers' and constructors' championships, have endured a miserable time of it in recent years.
They have not won a race since Jenson Button triumphed at the Brazilian Grand Prix in 2012 and finished a lowly sixth in last season's constructors' championship.
McLaren are entering the third year of a 10-year deal with Honda, and while both sides publicly insist they have no intention to pull the plug, their on-track troubles are significantly harming both brands.
Alonso, who has won 32 races in a career which yielded the last of his two championships more than a decade ago, is out of contract at the end of the season. And the 35-year-old, who staged talks with Mercedes over their recent vacancy following Nico Rosberg's retirement, has said he would take a decision on his next move after the summer break.
"I think Fernando is being honest with us, just as we're being honest with him," Boullier added.
"He first wanted to see how the new car was and how the new regulations are. He likes the new F1 and he wants to be competitive because he has talent to show the world and to himself.
"We need to be competitive to keep him happy."