At a press conference in Brussels ahead of a NATO meeting on the level of defense ministers, Stoltenberg said recent EU initiatives for defense cooperation within the bloc could benefit the NATO alliance if it did not enter into competition with it.
"More European defense spending and capabilities can strengthen NATO and contribute to fairer burden-sharing, but only if the EU's efforts are developed as a complement and not an alternative to NATO," Stoltenberg said.
For the European Union, common European defense has been a critical theme of the shift away from dependence on the United States, with the November 2017 signing and December 2017 launch of the Permanent Structured Cooperation (PESCO) agreement.
The PESCO pact will allow 25 participating EU member states to pursue greater cooperation on matters of defense and security.
In the Q&A session that followed his briefing, Stoltenberg stressed European commitment to the NATO, as well as how the continent's defense relied on the alliance.
"It will be absolutely without any meaning if EU and NATO started to compete because we share the same members," NATO chief said, adding: "90 percent of the people living in EU live in a NATO country -- more than 90 percent."
"The protection of Europe is dependent on NATO, especially after Brexit. 80 percent of NATO's defense expenditures will come from non-EU allies," said the NATO chief and former prime minister of Norway, which is non-EU member of the alliance.
For Stoltenberg, an example of possible problems came from the possibility of EU defense operations creating a list of capability requirements for its members that was in contradiction with a similar list from NATO, leading to incoherence.
"We are only one set of forces and we cannot have two lists of conflicting capability requirements," he said.
Stoltenberg's warning came on the same day that the United States gave a warning against European defense initiatives leading to consolidation of the European defense industry that would ultimately create discrimination for American defense companies.
US envoy to NATO Kay Bailey Hutchison warned on Tuesday against defense "protectionism", according to local media reports.
"Certainly we do not want this to be a protectionist vehicle for the EU and we are going to watch carefully because, if that becomes the case, then it could splinter the strong security alliance that we have," she told reporters in Brussels. "We want the Europeans to have capabilities and strength, but not to fence off American products."
US President Donald Trump has repeatedly criticized European NATO allies since just before his inauguration in January 2017 on what he has characterized as a lack of fair-burden sharing in defense spending, with only 3 allies meeting a 2 percent spending target in 2014.
The latest concerns from the Trump administration seemed to indicate that the US wanted to make sure European allies were not pulling away from the alliance.
PESCO and other European Defense Union initiatives have been presented as complements to NATO -- foremost a defense alliance -- but observers have noted that they represent a general change in political orientation, with European allies less confident of support and cooperation from the United States.
Asked to comment on these criticisms from the US during his conference, Stoltenberg said, "We have to avoid new barriers inside NATO."
"What we would welcome is a more competitive defense industry because that will benefit all NATO allies," he said.
Defense ministers of the NATO allies will meet on Wednesday and Thursday in Brussels, to discuss updates to the NATO command structure, increases in fair burden sharing, and NATO-EU cooperation, among other topics.