The league and the NFL Referees Association have yet to reach an agreement, and Goodell acknowledged Thursday that time was running out to make the regular officials available for the openers.
"We're anxious to get a deal done, but it has to get done that it's going to help us for the long term," Goodell said at a fantasy football event in Times Square. "It's not a short-term issue."
Of the replacement refs who have been calling preseason games, Goodell said: "We think they'll do a very credible job."
Officials probably need a week to 10 days to prepare for the season, Goodell said, and the first game is Sept. 5, 13 days away. The first full Sunday of games is Sept. 9.
NFLRA lead negotiator Mike Arnold said Thursday that officials have been training on their own during the lockout and would need less than a week to prep.
"We're ready to go," he said.
While the NFL and officials disagree on some financial matters, Goodell also characterized the differences as "philosophical." The NFL's proposal includes making some refs full-time — currently all game officials work part-time with outside jobs — and adding more crews.
Arnold said that the union was open to discussing such issues but any proposal to increase the number of officials while decreasing the pay for current refs was not viable.
Increasing the pool of officials would allow the league to replace individual officials or entire crews that are not performing well, Goodell said.
"Then it's based on performance, which is what fans all want, players all want, coaches all want," he said.
The replacement officials have been closely scrutinized during the preseason, with any error quickly pointed out by media and fans.
"It's not our job to judge the replacements, because their performance speaks for itself," Arnold said.
Goodell said he wasn't concerned that teams and fans would question the credibility of results if that inevitable first disputed call of the season takes place while replacement officials are on the field.
"We have controversial calls. Officiating is an imperfect science," he said. "They're not going to be correct all the time, but we have systems in place to try to help. We have instant replay, as an example, to try to help correct those mistakes. ... It's like any game. We get calls every Monday from fans, from coaches, from teams upset about a particular call. That happens. And it will happen going forward regardless of who's on the field."