Hagel's comments came after pro-Kremlin gunmen seized regional administration buildings in Crimea and Moscow ordered snap combat readiness drills near the border with the ex-Soviet state.
"I am closely watching the Russian military exercise... I expect them to be transparent about these activities," Hagel said.
"I urge them not to take steps that could be misinterpreted or lead to miscalculation," Hagel told a press conference at the close of a two-day NATO defence ministers meeting.
The crisis in Ukraine dominated the gathering, with an emergency meeting of the NATO-Ukraine Commission added to the agenda at the last moment.
Hagel said Washington was concerned about the latest developments, especially in Crimea, and was continuing "to talk to our Russian counterparts" about their intentions.
Just before Hagel spoke, NATO head Anders Fogh Rasmussen said he had no indication that Russia planned military intervention in Ukraine after he too had warned Moscow against fuelling tensions or creating misunderstandings.
"We have no information indicating that Russia has any plans to intervene militarily," Rasmussen said.
Asked about the military exercise, he said: "The Russians informed us about this and made clear that this exercise has nothing to do with ongoing events in Ukraine."
But the military exercise "does not make things easier", he added.
The NATO chief called on all parties to do their best to calm the situation.
"We need steps that can cool down the whole situation and that's a responsibility for all parties involved," he said.
NATO defence ministers on Wednesday agreed a statement which said a sovereign, independent and stable Ukraine was essential to security in Europe.
Rasmussen said after that statement that "Ukraine is the most important security issue in Europe today."
The latest developments have stoked concern about Ukraine's future and the possible wider fallout after the weekend ouster of pro-Russian president Viktor Yanukovych following three months of anti-government protests.
Crimea is especially sensitive as the home base for Russia's Black Sea fleet and tensions there took on a new dimension after Russian President Vladimir Putin ordered military preparedness checks in western Russia on Wednesday.
Ukraine's new interim government on Thursday warned the Russian navy to keep its troops in their bases.
"Any troop movements will be considered as military aggression," acting pro-Western president Oleksandr Turchynov told parliament.
Moscow for its part said it would abide by the treaties governing the use of Crimea by its Black Sea fleet.