Chinese shares slipped on fears over the economy as well as liquidity after authorities unveiled a list of 28 firms that have filed for initial public offerings.
Tokyo finished flat, giving up 3.89 points to 14,512.38, Seoul was down 0.25%, or 5.06 points, at 1,999.22, while Taipei ended 0.17%, or 15.47 points, lower at 8,951.19. Shanghai tumbled 1.52%, or 31.92 points, to 2,065.83.
Singapore was flat in afternoon trade.
Hong Kong, Sydney and Wellington were closed for the Easter holidays.
With markets in most of Europe and the United States closed on Friday and Monday, business was thin as investors look ahead to the release this week of preliminary manufacturing data from around the world as well as US retail and house price figures.
In afternoon trade, the dollar was at 102.55 yen compared with 102.41 yen on Friday, while the euro bought $1.3825 and 141.76 yen, against $1.3817 and 141.48 yen.
In Tokyo, the government said Japan's trade deficit hit $14 billion (1.45 trillion yen) in March, compared with a shortfall of 356.9 billion yen a year ago.
The huge deficit came as a weaker yen increased the cost of imports, especially of fossil fuels, and was compounded by the fact consumers rushed to buy ahead of the April 1 sales tax hike.
This week will see the start of corporate reporting for the first three months of 2014, with investors paying close attention to Japanese firms' outlook following the sales tax rise, which critics fear could derail the economy's young recovery.
"It's difficult to project an impact from the consumption tax increase. Companies are likely to report conservative guidance," Shigeo Sugawara, senior investment officer at Sompo Japan Nipponkoa Asset Management, told Dow Jones Newswires.
In China, the stock regulator at the weekend said several firms were planning IPOs, state media reported, sparking worries that floodgates were opening after a two-month pause in new listings.
On oil markets New York's main contract, West Texas Intermediate for May delivery, dipped 13 cents to $104.17 in afternoon trade and Brent North Sea crude for June eased 42 cents to $109.11 a barrel.
Gold fetched $1,286.69 an ounce at 0710 GMT, compared with $1,289.90 on Friday.