When it gets to the point where an Army lieutenant colonel takes home more pay than a member of Congress, even some of the most defense-minded lawmakers start asking questions.

House Budget Committee Chairman James R. Jones (D-Okla.) did just that yesterday. He had before him statistics indicating that military pay raises recommended by President Reagan to take effect later this year will leave Washington-based lieutenant colonels with more money in their pockets than either members of Congress or the secretary of the Army.

Moreover, Jones pointed out, even Army majors based in the Washington area would take home more pay than legislators is Defense Secretary Caspar W. Weinberger prevails in his recommendation to make the first $20,000 of military salaries exempt from federal income taxes. And a lieutenant colonel would then make more than the secretary of defense.

While stopping short of opposing the military pay raises, Jones said he thinks it may be time to stop "scatter-gun across-the-board" increases in favor of more selective ones targeted at attracting and retaining specific groups of skilled people currently in short supply. Sen. Sam Nunn (D-Ga.), one of the chief congressional proponents of military pay increases, has recently been voicing similar thoughts.

Jones said he hasn't made up his mind yet but is exploring the idea of recommending a new system of selective pay increases and trying to cut out the 5.3 percent across-the-board military pay increase that is planned for July. The July increase could be eliminated as part of the spending-cut package that Congress is assembling at Reagan's behest, for a savings of $2 billion for fiscal 1982.

Occasional reports of low-paid servicemen qualifying for food stamps, coupled with the generally hawkish mood of Congress, have combined to improve the prospects for military pay proposals in Congress recently. But the signals from Jones and Nunn, coupled with invidious comparisons with congressional pay, may well prompt pressure for a more targeted system of military pay.

According to statistics compiled by the Congressional Budget Office at the request of a House Budget Committee task force, a lieutenant colonel would receive an annual base pay of $36,597 after the 5.3 percent increase in July and another 9.1 percent increase that Reagan has recommended for October. This is substantially less than the $60,663 salary a member of Congress gets.

However, with the tax-free living allowances that military people also receive and without the health and pension contributions that members of Congress and other civilian government employes must make, a lieutenant colonel who has been in the service for 20 years and lives in the Washington area would take home $35,570, compared to a legislator's take-home pay of $33,958, according to the CBO.

The CBO figures break down this way: the Washington-based lieutenant colonel would add to his $36,597 base pay a $1,138 subsistence allowance, a $5,877 allowance for family housing and $2,938 to help cover the high cost of living in the Washington area. The officer also makes no retirement or health insurance contributions, in contrast to the member of Congress, who pays $4,853 for retirement and $794 for health insurance.

With a $20,000 tax exemption, the lieutenant colonel would take home $41,222 and a major $35,946, according to the CBO.

The CBO report cited similar take-home pay computations for other military ranks as well as civilian government job levels. For instance, a private takes home $12,121, a sergeant $15,995, a master sergeant $23,105, a second lieutenant $16,985, a major $31,243, a full colonel $41,637 and a brigadier general $44,886.

By way of contrast, a GS Grade 15, 4th step, takes home $30,529, less than a major. A GS 9, 4th step, takes home $15,766, less than a sergeant. In the private sector, according to Bureau of Labor Statistics figures cited by the Budget Committee, the average after-tax wage among nonsupervisory manufacturing workers was $13,852 a year as of February. For construction workers it was $16,523. In finance, insurance and real estate it was $10,045, in mining, $17,834.

Congressional budget officials cautioned that the figures were "not necessarily representative" of the various groups, noting that they assumed standard deductions and included no outside income or special military benefits like sea pay. The CBO analysis also did not have comparative figures pegged to present military compensation, but a CBO official said a member of Congress and a lieutenant colonel currently receive about the same take-home pay.