"Negotiations are ongoing and they are going very well," the American told reporters at the Italian Grand Prix. "But you've got to have a Plan B and C in the event you don't reach an agreement. And we've got those plans."
Double world champion Alonso, who is out of contract at the end of the year, is reportedly considering his options after becoming frustrated with Honda's inability to produce a competitive engine. Both the Spaniard and the team have denied, however, that he has told them that he will not stay if the team sticks with the Japanese manufacturer.
McLaren's engine options appear to be as limited as Alonso's, however.
McLaren's only realistic alternative to Honda is Renault, if Red Bull-owned Toro Rosso free up a supply of the French manufacturer's power units by switching to Honda.
The only teams who might be in a position to offer the 36-year-old a seat - notably Williams, Renault or Force India - have either not won a race in years or not at all. Renault F1 bosses were seen entering the McLaren motorhome at Monza on Friday, increasing speculation that a deal was being struck, although Brown made light of the situation.
"They have my Lotus 98T engine that I'm waiting for them to rebuild, so I was asking about that," he said. "They do have it, that's a fact." He would not comment on any talks with Honda.
Some media reports have indicated that Toro Rosso need a decision this weekend but Brown said that was not the case for McLaren.
"Nothing's finalised," he said. "We don't have to make a decision this weekend. I can't speak for Toro Rosso."
Brown said the decision would be a sporting one primarily with McLaren, who last won a race in 2012, needing to be back on the podium. He did not rule out Honda raising their game in time for next season.
"They're spending more money, so they're doing what it takes to be more competitive. They're doing different stuff now... they've acknowledged they are working with some outside consultants," he said.
"We are going to sit down next week with guys that are much smarter on power units than myself and take a view on what we see their plans are and what they've accomplished and then take a view," added Brown (Reporting by Alan Baldwin; Editing by Christian Radnedge)