Merrill Lynch & Co. and four telephone companies yesterday began a plan that is expected to significantly reduce the number of stockholders holding fewer than 100 shares in any of the four companies.

Under the plan, the shareholders will be able to sell their stock through Merrill Lynch at a discounted brokerage fee. The program is expected to give Merrill Lynch big-volume business and allow the four companies to shed a large number of odd-lot stockholders whose accounts carry high administrative costs.

The 2.8 million odd-lot shareholders in the four companies -- AT&T, Bell Atlantic Corp., BellSouth Corp. and American Information Technologies Corp. (Ameritech) -- will have the chance to dispose of their holdings without paying high transaction fees.

With the break-up of AT&T on Jan. 1, 1984, investors holding 10 or more of its shares retained those shares and got one share in each of the seven regional operating companies, the "Baby Bells." Investors with fewer than 10 shares kept them and got a cash payment for their interest in the operating companies.

In general, the companies have done well on the markets.

Bell Atlantic, for instance, closed at $33.56 (adjusted for subsequent splits) on Jan. 3, 1984, the first trading day after it came into existence. It finished yesterday at $73.37 1/2. The other three companies have shown similar gains.

Investors who hold a small number of shares of the companies often do not want to sell because commissions would eat up much of the proceeds, according to Tom Healey, spokesman for Bell Atlantic.

Under the Merrill Lynch program, they will pay $6 per company traded and 30 cents per share, considerably less than normal fees.

Merrill Lynch will sell the shares on the open market, and the seller's price will be the average of all shares of each company sold under the program on a given day. The program runs until Dec. 7.

The companies say they are not trying to "weed out" small shareholders, but the companies do stand to gain considerably by their departure.

Federal law requires costly services for each shareholder, such as quarterly earnings reports, an annual report and information on the annual meeting.

Bell companies have had similar programs in the past. Bell Atlantic, for instance, has shed about 220,000 accounts with such plans.

However, it still has about 1,020,000 of them holding 14 percent of its total shares and is eager to get the number down further.